Starting phenix.real_space_refine on Sun Sep 29 02:11:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/09_2024/8sew_40431.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/09_2024/8sew_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/09_2024/8sew_40431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/09_2024/8sew_40431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/09_2024/8sew_40431.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/09_2024/8sew_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 11.97, per 1000 atoms: 0.58 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " 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=0, symmetry=0 Time building additional restraints: 4.88 Conformation dependent library (CDL) restraints added in 2.3 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: 2.24 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: 6.14 Time building geometry restraints manager: 5.69 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: 12206 30.20 - 60.41: 225 60.41 - 90.61: 12 90.61 - 120.81: 4 120.81 - 151.01: 4 Dihedral angle restraints: 12451 sinusoidal: 5103 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 12448 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: 16 1.19 - 2.12: 39 2.12 - 3.05: 13635 3.05 - 3.97: 54823 3.97 - 4.90: 102550 Warning: very small nonbonded interaction distances. Nonbonded interactions: 171063 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=" NZ LYS B4581 " pdb=" CB ASP C4878 " model vdw 0.440 3.520 ... (remaining 171058 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 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: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 46.650 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.510 ------------------------------------------------------------------------------- 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 : 0.004 0.112 21208 Z= 0.278 Angle : 0.591 13.737 28644 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 *********************** 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 fitting. rotamer outliers: 48 poor density : 464 time to evaluate : 2.389 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: 1.2074 time to fit residues: 696.8461 Evaluate side-chains 396 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 364 time to evaluate : 2.402 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.5980 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21208 Z= 0.175 Angle : 0.553 7.240 28644 Z= 0.282 Chirality : 0.038 0.138 3096 Planarity : 0.004 0.049 3612 Dihedral : 10.012 144.294 2812 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.03 % Allowed : 12.70 % Favored : 84.27 % 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: 2.25 (0.17), residues: 2476 helix: 2.16 (0.12), residues: 1700 sheet: 0.19 (0.48), residues: 112 loop : 0.01 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B3986 HIS 0.004 0.001 HIS D3994 PHE 0.018 0.001 PHE C4916 TYR 0.009 0.001 TYR D5014 ARG 0.008 0.001 ARG C4189 *********************** 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 463 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 395 time to evaluate : 2.449 Fit side-chains REVERT: A 3969 ILE cc_start: 0.8632 (pt) cc_final: 0.8420 (pt) REVERT: A 4023 MET cc_start: 0.7587 (ttp) cc_final: 0.7015 (tpp) REVERT: A 4042 ARG cc_start: 0.6812 (mtm110) cc_final: 0.6326 (mtm180) REVERT: A 4196 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5904 (tp30) REVERT: A 4550 LYS cc_start: 0.7823 (tppt) cc_final: 0.7299 (pptt) REVERT: A 4580 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6289 (t80) REVERT: A 4992 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8344 (mt) REVERT: B 3969 ILE cc_start: 0.8630 (pt) cc_final: 0.8420 (pt) REVERT: B 4023 MET cc_start: 0.7586 (ttp) cc_final: 0.7015 (tpp) REVERT: B 4042 ARG cc_start: 0.6811 (mtm110) cc_final: 0.6327 (mtm180) REVERT: B 4196 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5907 (tp30) REVERT: B 4550 LYS cc_start: 0.7829 (tppt) cc_final: 0.7304 (pptt) REVERT: B 4580 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6287 (t80) REVERT: B 4992 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8343 (mt) REVERT: C 3969 ILE cc_start: 0.8631 (pt) cc_final: 0.8421 (pt) REVERT: C 4023 MET cc_start: 0.7586 (ttp) cc_final: 0.7018 (tpp) REVERT: C 4042 ARG cc_start: 0.6813 (mtm110) cc_final: 0.6327 (mtm180) REVERT: C 4196 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5906 (tp30) REVERT: C 4550 LYS cc_start: 0.7824 (tppt) cc_final: 0.7301 (pptt) REVERT: C 4580 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6285 (t80) REVERT: C 4992 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8342 (mt) REVERT: D 3969 ILE cc_start: 0.8635 (pt) cc_final: 0.8422 (pt) REVERT: D 4023 MET cc_start: 0.7589 (ttp) cc_final: 0.7018 (tpp) REVERT: D 4042 ARG cc_start: 0.6809 (mtm110) cc_final: 0.6324 (mtm180) REVERT: D 4196 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5905 (tp30) REVERT: D 4550 LYS cc_start: 0.7827 (tppt) cc_final: 0.7305 (pptt) REVERT: D 4580 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6284 (t80) REVERT: D 4992 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8344 (mt) outliers start: 68 outliers final: 16 residues processed: 431 average time/residue: 1.3275 time to fit residues: 645.4564 Evaluate side-chains 397 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 369 time to evaluate : 2.259 ------------------------------------------------------------------------------- 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 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 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 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 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 125 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 0.0970 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4043 GLN A4973 HIS A5031 GLN B4043 GLN B4973 HIS B5031 GLN C4043 GLN C4973 HIS C5031 GLN D4043 GLN D4973 HIS D5031 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21208 Z= 0.172 Angle : 0.513 6.440 28644 Z= 0.263 Chirality : 0.037 0.134 3096 Planarity : 0.004 0.053 3612 Dihedral : 9.428 146.001 2784 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.57 % Allowed : 13.50 % Favored : 82.93 % 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: 2.30 (0.17), residues: 2476 helix: 2.18 (0.12), residues: 1724 sheet: -0.11 (0.47), residues: 112 loop : 0.09 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A4701 HIS 0.003 0.001 HIS D3994 PHE 0.018 0.001 PHE A4916 TYR 0.015 0.001 TYR A5032 ARG 0.010 0.001 ARG D4189 *********************** 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 463 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 383 time to evaluate : 2.303 Fit side-chains REVERT: A 3955 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7137 (mtm) REVERT: A 3986 TRP cc_start: 0.8402 (m100) cc_final: 0.7841 (m100) REVERT: A 3992 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: A 4023 MET cc_start: 0.7447 (ttp) cc_final: 0.7232 (tpp) REVERT: A 4042 ARG cc_start: 0.6659 (mtm110) cc_final: 0.6078 (mtm180) REVERT: A 4196 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5747 (tp30) REVERT: A 4212 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 4224 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7305 (pt0) REVERT: A 4580 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6241 (t80) REVERT: A 4992 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8359 (mt) REVERT: B 3955 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7131 (mtm) REVERT: B 3986 TRP cc_start: 0.8398 (m100) cc_final: 0.7837 (m100) REVERT: B 3992 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: B 4023 MET cc_start: 0.7440 (ttp) cc_final: 0.7224 (tpp) REVERT: B 4042 ARG cc_start: 0.6661 (mtm110) cc_final: 0.6086 (mtm180) REVERT: B 4196 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5750 (tp30) REVERT: B 4212 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: B 4224 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: B 4580 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6239 (t80) REVERT: B 4992 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8356 (mt) REVERT: C 3955 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7141 (mtm) REVERT: C 3986 TRP cc_start: 0.8400 (m100) cc_final: 0.7840 (m100) REVERT: C 3992 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: C 4023 MET cc_start: 0.7444 (ttp) cc_final: 0.7229 (tpp) REVERT: C 4042 ARG cc_start: 0.6658 (mtm110) cc_final: 0.6079 (mtm180) REVERT: C 4196 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5750 (tp30) REVERT: C 4212 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: C 4224 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7302 (pt0) REVERT: C 4580 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6237 (t80) REVERT: C 4992 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8358 (mt) REVERT: D 3955 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7134 (mtm) REVERT: D 3986 TRP cc_start: 0.8401 (m100) cc_final: 0.7843 (m100) REVERT: D 3992 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: D 4023 MET cc_start: 0.7445 (ttp) cc_final: 0.7227 (tpp) REVERT: D 4042 ARG cc_start: 0.6656 (mtm110) cc_final: 0.6080 (mtm180) REVERT: D 4196 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5748 (tp30) REVERT: D 4212 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: D 4224 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7302 (pt0) REVERT: D 4580 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6238 (t80) REVERT: D 4992 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8358 (mt) outliers start: 80 outliers final: 20 residues processed: 423 average time/residue: 1.3243 time to fit residues: 633.2160 Evaluate side-chains 407 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 359 time to evaluate : 2.558 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 222 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21208 Z= 0.189 Angle : 0.528 7.480 28644 Z= 0.268 Chirality : 0.037 0.136 3096 Planarity : 0.004 0.051 3612 Dihedral : 9.167 147.397 2776 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.02 % Favored : 97.82 % Rotamer: Outliers : 3.57 % Allowed : 14.13 % Favored : 82.31 % 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: 2.18 (0.12), residues: 1720 sheet: -0.32 (0.47), residues: 112 loop : 0.01 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A5019 HIS 0.003 0.001 HIS A3994 PHE 0.019 0.001 PHE A4916 TYR 0.009 0.001 TYR B5032 ARG 0.010 0.001 ARG D4189 *********************** 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 436 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 356 time to evaluate : 2.586 Fit side-chains REVERT: A 3955 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7148 (mtm) REVERT: A 3959 LYS cc_start: 0.6581 (tttp) cc_final: 0.6291 (tttp) REVERT: A 3980 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7654 (mm) REVERT: A 4023 MET cc_start: 0.7465 (ttp) cc_final: 0.7228 (tpp) REVERT: A 4042 ARG cc_start: 0.6597 (mtm110) cc_final: 0.6046 (mtm180) REVERT: A 4196 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5745 (tp30) REVERT: A 4209 GLN cc_start: 0.7806 (pt0) cc_final: 0.7500 (pm20) REVERT: A 4212 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: A 4224 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7320 (pt0) REVERT: A 4580 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6298 (t80) REVERT: A 4704 LEU cc_start: 0.8967 (tp) cc_final: 0.8362 (mm) REVERT: A 4992 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8378 (mt) REVERT: B 3955 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7128 (mtm) REVERT: B 3959 LYS cc_start: 0.6576 (tttp) cc_final: 0.6289 (tttp) REVERT: B 3980 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7657 (mm) REVERT: B 4023 MET cc_start: 0.7458 (ttp) cc_final: 0.7219 (tpp) REVERT: B 4042 ARG cc_start: 0.6598 (mtm110) cc_final: 0.6054 (mtm180) REVERT: B 4196 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5746 (tp30) REVERT: B 4209 GLN cc_start: 0.7805 (pt0) cc_final: 0.7500 (pm20) REVERT: B 4212 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: B 4224 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: B 4580 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6297 (t80) REVERT: B 4704 LEU cc_start: 0.8966 (tp) cc_final: 0.8362 (mm) REVERT: B 4874 MET cc_start: 0.7126 (mmm) cc_final: 0.6879 (mmm) REVERT: B 4992 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8377 (mt) REVERT: C 3955 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7134 (mtm) REVERT: C 3959 LYS cc_start: 0.6584 (tttp) cc_final: 0.6293 (tttp) REVERT: C 3980 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7656 (mm) REVERT: C 4023 MET cc_start: 0.7465 (ttp) cc_final: 0.7228 (tpp) REVERT: C 4042 ARG cc_start: 0.6594 (mtm110) cc_final: 0.6051 (mtm180) REVERT: C 4196 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5746 (tp30) REVERT: C 4209 GLN cc_start: 0.7806 (pt0) cc_final: 0.7499 (pm20) REVERT: C 4212 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: C 4224 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: C 4580 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6296 (t80) REVERT: C 4704 LEU cc_start: 0.8965 (tp) cc_final: 0.8361 (mm) REVERT: C 4874 MET cc_start: 0.7120 (mmm) cc_final: 0.6872 (mmm) REVERT: C 4992 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8375 (mt) REVERT: D 3955 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7130 (mtm) REVERT: D 3959 LYS cc_start: 0.6581 (tttp) cc_final: 0.6294 (tttp) REVERT: D 3980 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7655 (mm) REVERT: D 4023 MET cc_start: 0.7464 (ttp) cc_final: 0.7225 (tpp) REVERT: D 4042 ARG cc_start: 0.6595 (mtm110) cc_final: 0.6049 (mtm180) REVERT: D 4196 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5749 (tp30) REVERT: D 4209 GLN cc_start: 0.7808 (pt0) cc_final: 0.7502 (pm20) REVERT: D 4212 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: D 4224 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: D 4580 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6241 (t80) REVERT: D 4704 LEU cc_start: 0.8966 (tp) cc_final: 0.8362 (mm) REVERT: D 4874 MET cc_start: 0.7116 (mmm) cc_final: 0.6868 (mmm) REVERT: D 4992 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8377 (mt) outliers start: 80 outliers final: 24 residues processed: 412 average time/residue: 1.3164 time to fit residues: 613.6917 Evaluate side-chains 399 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 347 time to evaluate : 2.411 ------------------------------------------------------------------------------- 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 4224 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 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 4224 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 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 4224 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 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 4224 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 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 199 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 178 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 204 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 122 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4973 HIS B4973 HIS C4973 HIS D4973 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21208 Z= 0.165 Angle : 0.526 7.855 28644 Z= 0.263 Chirality : 0.036 0.133 3096 Planarity : 0.004 0.070 3612 Dihedral : 9.146 148.314 2776 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.52 % Allowed : 14.88 % Favored : 81.60 % 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: 2.24 (0.12), residues: 1716 sheet: -0.50 (0.47), residues: 112 loop : -0.11 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C5019 HIS 0.002 0.001 HIS A3994 PHE 0.018 0.001 PHE A4916 TYR 0.008 0.001 TYR A5032 ARG 0.011 0.001 ARG D4736 *********************** 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 446 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 367 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3955 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7146 (mtm) REVERT: A 3959 LYS cc_start: 0.6560 (tttp) cc_final: 0.6280 (tttp) REVERT: A 3986 TRP cc_start: 0.8411 (m100) cc_final: 0.8084 (m100) REVERT: A 4042 ARG cc_start: 0.6578 (mtm110) cc_final: 0.5959 (mtm180) REVERT: A 4196 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5554 (tp30) REVERT: A 4209 GLN cc_start: 0.7777 (pt0) cc_final: 0.7473 (pm20) REVERT: A 4212 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: A 4580 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6283 (t80) REVERT: A 4704 LEU cc_start: 0.8962 (tp) cc_final: 0.8353 (mm) REVERT: A 4911 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7464 (mm) REVERT: A 4992 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8380 (mt) REVERT: B 3955 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7163 (mtm) REVERT: B 3959 LYS cc_start: 0.6552 (tttp) cc_final: 0.6275 (tttp) REVERT: B 3986 TRP cc_start: 0.8410 (m100) cc_final: 0.8083 (m100) REVERT: B 4042 ARG cc_start: 0.6578 (mtm110) cc_final: 0.5962 (mtm180) REVERT: B 4196 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5558 (tp30) REVERT: B 4209 GLN cc_start: 0.7774 (pt0) cc_final: 0.7472 (pm20) REVERT: B 4212 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: B 4580 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6277 (t80) REVERT: B 4704 LEU cc_start: 0.8962 (tp) cc_final: 0.8353 (mm) REVERT: B 4874 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6820 (mmm) REVERT: B 4911 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7471 (mm) REVERT: B 4992 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8379 (mt) REVERT: C 3955 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7174 (mtm) REVERT: C 3959 LYS cc_start: 0.6560 (tttp) cc_final: 0.6284 (tttp) REVERT: C 3986 TRP cc_start: 0.8413 (m100) cc_final: 0.8085 (m100) REVERT: C 4042 ARG cc_start: 0.6573 (mtm110) cc_final: 0.5954 (mtm180) REVERT: C 4196 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5561 (tp30) REVERT: C 4209 GLN cc_start: 0.7775 (pt0) cc_final: 0.7469 (pm20) REVERT: C 4212 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: C 4580 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6278 (t80) REVERT: C 4704 LEU cc_start: 0.8960 (tp) cc_final: 0.8351 (mm) REVERT: C 4874 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6812 (mmm) REVERT: C 4911 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7472 (mm) REVERT: C 4992 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8379 (mt) REVERT: D 3955 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7170 (mtm) REVERT: D 3959 LYS cc_start: 0.6555 (tttp) cc_final: 0.6277 (tttp) REVERT: D 3986 TRP cc_start: 0.8411 (m100) cc_final: 0.8084 (m100) REVERT: D 4042 ARG cc_start: 0.6575 (mtm110) cc_final: 0.5955 (mtm180) REVERT: D 4196 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5557 (tp30) REVERT: D 4209 GLN cc_start: 0.7779 (pt0) cc_final: 0.7469 (pm20) REVERT: D 4212 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: D 4580 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6276 (t80) REVERT: D 4704 LEU cc_start: 0.8962 (tp) cc_final: 0.8352 (mm) REVERT: D 4874 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6809 (mmm) REVERT: D 4911 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7472 (mm) REVERT: D 4992 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8379 (mt) outliers start: 79 outliers final: 20 residues processed: 419 average time/residue: 1.3122 time to fit residues: 624.6770 Evaluate side-chains 410 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 363 time to evaluate : 2.212 ------------------------------------------------------------------------------- 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 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 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 4196 GLU Chi-restraints excluded: chain B residue 4212 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 B residue 4874 MET 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 4196 GLU Chi-restraints excluded: chain C residue 4212 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 C residue 4874 MET 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 4196 GLU Chi-restraints excluded: chain D residue 4212 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 Chi-restraints excluded: chain D residue 4874 MET 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 80 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 140 optimal weight: 0.0970 chunk 59 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21208 Z= 0.144 Angle : 0.509 8.123 28644 Z= 0.252 Chirality : 0.036 0.133 3096 Planarity : 0.004 0.065 3612 Dihedral : 9.103 148.648 2776 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.67 % Allowed : 16.09 % Favored : 81.24 % 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: 2.34 (0.17), residues: 2476 helix: 2.31 (0.12), residues: 1720 sheet: -0.43 (0.47), residues: 112 loop : -0.15 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A5019 HIS 0.002 0.001 HIS A3994 PHE 0.019 0.001 PHE A4922 TYR 0.014 0.001 TYR A4687 ARG 0.013 0.001 ARG A4189 *********************** 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 444 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 384 time to evaluate : 2.453 Fit side-chains REVERT: A 3955 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7166 (mtm) REVERT: A 3959 LYS cc_start: 0.6528 (tttp) cc_final: 0.6226 (tttp) REVERT: A 3986 TRP cc_start: 0.8338 (m100) cc_final: 0.8096 (m100) REVERT: A 4042 ARG cc_start: 0.6567 (mtm110) cc_final: 0.5978 (mtm180) REVERT: A 4196 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5598 (tp30) REVERT: A 4212 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: A 4580 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.6372 (t80) REVERT: A 4992 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8362 (mt) REVERT: B 3959 LYS cc_start: 0.6519 (tttp) cc_final: 0.6223 (tttp) REVERT: B 3986 TRP cc_start: 0.8336 (m100) cc_final: 0.8100 (m100) REVERT: B 4042 ARG cc_start: 0.6565 (mtm110) cc_final: 0.5983 (mtm180) REVERT: B 4196 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5602 (tp30) REVERT: B 4212 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: B 4580 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6338 (t80) REVERT: B 4874 MET cc_start: 0.7085 (mmm) cc_final: 0.6857 (mmm) REVERT: B 4992 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8362 (mt) REVERT: C 3959 LYS cc_start: 0.6529 (tttp) cc_final: 0.6228 (tttp) REVERT: C 3986 TRP cc_start: 0.8336 (m100) cc_final: 0.8100 (m100) REVERT: C 4042 ARG cc_start: 0.6561 (mtm110) cc_final: 0.5977 (mtm180) REVERT: C 4196 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5603 (tp30) REVERT: C 4212 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: C 4580 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6339 (t80) REVERT: C 4874 MET cc_start: 0.7079 (mmm) cc_final: 0.6853 (mmm) REVERT: C 4992 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8361 (mt) REVERT: D 3959 LYS cc_start: 0.6523 (tttp) cc_final: 0.6221 (tttp) REVERT: D 3986 TRP cc_start: 0.8334 (m100) cc_final: 0.8097 (m100) REVERT: D 4042 ARG cc_start: 0.6562 (mtm110) cc_final: 0.5976 (mtm180) REVERT: D 4196 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5601 (tp30) REVERT: D 4212 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: D 4580 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6344 (t80) REVERT: D 4874 MET cc_start: 0.7074 (mmm) cc_final: 0.6847 (mmm) REVERT: D 4992 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8361 (mt) outliers start: 60 outliers final: 24 residues processed: 424 average time/residue: 1.2292 time to fit residues: 593.5390 Evaluate side-chains 407 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 366 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4720 VAL 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 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4720 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 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4720 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 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4720 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 110 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: A4034 ASN B4034 ASN C4034 ASN C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21208 Z= 0.207 Angle : 0.559 8.102 28644 Z= 0.278 Chirality : 0.037 0.135 3096 Planarity : 0.004 0.070 3612 Dihedral : 9.182 149.738 2776 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.21 % Allowed : 16.09 % Favored : 80.70 % 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: 2.22 (0.17), residues: 2476 helix: 2.26 (0.12), residues: 1696 sheet: -0.59 (0.46), residues: 112 loop : -0.18 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B5019 HIS 0.003 0.001 HIS D4886 PHE 0.023 0.001 PHE B4922 TYR 0.019 0.001 TYR B4687 ARG 0.014 0.001 ARG D4736 *********************** 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 455 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 383 time to evaluate : 2.464 Fit side-chains REVERT: A 3959 LYS cc_start: 0.6690 (tttp) cc_final: 0.6343 (tttp) REVERT: A 3986 TRP cc_start: 0.8354 (m100) cc_final: 0.8126 (m100) REVERT: A 4042 ARG cc_start: 0.6515 (mtm110) cc_final: 0.6005 (mtm180) REVERT: A 4045 VAL cc_start: 0.7536 (OUTLIER) cc_final: 0.7284 (m) REVERT: A 4196 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5876 (tp30) REVERT: A 4209 GLN cc_start: 0.7781 (pt0) cc_final: 0.7472 (pm20) REVERT: A 4212 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: A 4224 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: A 4580 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.6401 (t80) REVERT: A 4911 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7455 (mm) REVERT: A 4992 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 3959 LYS cc_start: 0.6684 (tttp) cc_final: 0.6338 (tttp) REVERT: B 3986 TRP cc_start: 0.8354 (m100) cc_final: 0.8132 (m100) REVERT: B 4042 ARG cc_start: 0.6514 (mtm110) cc_final: 0.6007 (mtm180) REVERT: B 4045 VAL cc_start: 0.7540 (OUTLIER) cc_final: 0.7286 (m) REVERT: B 4196 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5878 (tp30) REVERT: B 4209 GLN cc_start: 0.7780 (pt0) cc_final: 0.7472 (pm20) REVERT: B 4212 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: B 4224 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: B 4580 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6398 (t80) REVERT: B 4874 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6835 (mmm) REVERT: B 4911 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7463 (mm) REVERT: B 4992 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8388 (mt) REVERT: C 3959 LYS cc_start: 0.6698 (tttp) cc_final: 0.6348 (tttp) REVERT: C 3986 TRP cc_start: 0.8354 (m100) cc_final: 0.8130 (m100) REVERT: C 4042 ARG cc_start: 0.6516 (mtm110) cc_final: 0.6004 (mtm180) REVERT: C 4045 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7283 (m) REVERT: C 4196 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5885 (tp30) REVERT: C 4209 GLN cc_start: 0.7781 (pt0) cc_final: 0.7470 (pm20) REVERT: C 4212 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: C 4224 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: C 4580 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6399 (t80) REVERT: C 4874 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6827 (mmm) REVERT: C 4911 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7462 (mm) REVERT: C 4992 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8386 (mt) REVERT: D 3959 LYS cc_start: 0.6692 (tttp) cc_final: 0.6343 (tttp) REVERT: D 3986 TRP cc_start: 0.8352 (m100) cc_final: 0.8125 (m100) REVERT: D 4042 ARG cc_start: 0.6513 (mtm110) cc_final: 0.6003 (mtm180) REVERT: D 4045 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7282 (m) REVERT: D 4196 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5876 (tp30) REVERT: D 4209 GLN cc_start: 0.7784 (pt0) cc_final: 0.7472 (pm20) REVERT: D 4212 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: D 4224 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7299 (pt0) REVERT: D 4580 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6398 (t80) REVERT: D 4874 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6825 (mmm) REVERT: D 4911 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7466 (mm) REVERT: D 4992 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8388 (mt) outliers start: 72 outliers final: 20 residues processed: 432 average time/residue: 1.2353 time to fit residues: 604.7256 Evaluate side-chains 404 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 353 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4224 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 4045 VAL 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 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 4874 MET 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 4045 VAL 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 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 4874 MET 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 4045 VAL 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 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 4874 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21208 Z= 0.178 Angle : 0.564 8.389 28644 Z= 0.277 Chirality : 0.037 0.134 3096 Planarity : 0.004 0.069 3612 Dihedral : 9.171 149.708 2776 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.74 % Favored : 98.10 % Rotamer: Outliers : 2.90 % Allowed : 16.58 % Favored : 80.53 % 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: 2.14 (0.17), residues: 2476 helix: 2.18 (0.12), residues: 1716 sheet: -0.64 (0.47), residues: 112 loop : -0.23 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D5019 HIS 0.003 0.001 HIS A3994 PHE 0.023 0.001 PHE A4922 TYR 0.015 0.001 TYR D4687 ARG 0.014 0.001 ARG B4189 *********************** 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 423 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 358 time to evaluate : 2.406 Fit side-chains REVERT: A 3959 LYS cc_start: 0.6659 (tttp) cc_final: 0.6322 (tttp) REVERT: A 3986 TRP cc_start: 0.8323 (m100) cc_final: 0.8095 (m100) REVERT: A 4042 ARG cc_start: 0.6354 (mtm110) cc_final: 0.5866 (mtm180) REVERT: A 4045 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7255 (m) REVERT: A 4196 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5738 (tp30) REVERT: A 4209 GLN cc_start: 0.7765 (pt0) cc_final: 0.7479 (pm20) REVERT: A 4212 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: A 4224 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: A 4580 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.6417 (t80) REVERT: A 4704 LEU cc_start: 0.8978 (tp) cc_final: 0.8379 (mm) REVERT: A 4736 ARG cc_start: 0.6924 (ttp-110) cc_final: 0.6518 (ttp-110) REVERT: A 4911 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7454 (mm) REVERT: A 4992 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8362 (mt) REVERT: B 3955 MET cc_start: 0.7439 (mmm) cc_final: 0.7189 (mmm) REVERT: B 3959 LYS cc_start: 0.6647 (tttp) cc_final: 0.6301 (tttp) REVERT: B 3986 TRP cc_start: 0.8322 (m100) cc_final: 0.8096 (m100) REVERT: B 4042 ARG cc_start: 0.6353 (mtm110) cc_final: 0.5868 (mtm180) REVERT: B 4045 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7255 (m) REVERT: B 4196 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5739 (tp30) REVERT: B 4209 GLN cc_start: 0.7763 (pt0) cc_final: 0.7480 (pm20) REVERT: B 4212 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: B 4224 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: B 4580 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.6415 (t80) REVERT: B 4704 LEU cc_start: 0.8976 (tp) cc_final: 0.8378 (mm) REVERT: B 4736 ARG cc_start: 0.6928 (ttp-110) cc_final: 0.6524 (ttp-110) REVERT: B 4874 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6834 (mmm) REVERT: B 4911 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7459 (mm) REVERT: B 4992 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8361 (mt) REVERT: C 3955 MET cc_start: 0.7442 (mmm) cc_final: 0.7193 (mmm) REVERT: C 3959 LYS cc_start: 0.6670 (tttp) cc_final: 0.6327 (tttp) REVERT: C 3986 TRP cc_start: 0.8323 (m100) cc_final: 0.8096 (m100) REVERT: C 4042 ARG cc_start: 0.6353 (mtm110) cc_final: 0.5865 (mtm180) REVERT: C 4045 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7255 (m) REVERT: C 4196 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5740 (tp30) REVERT: C 4209 GLN cc_start: 0.7765 (pt0) cc_final: 0.7478 (pm20) REVERT: C 4212 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: C 4224 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: C 4580 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6415 (t80) REVERT: C 4704 LEU cc_start: 0.8975 (tp) cc_final: 0.8377 (mm) REVERT: C 4736 ARG cc_start: 0.6924 (ttp-110) cc_final: 0.6520 (ttp-110) REVERT: C 4874 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6825 (mmm) REVERT: C 4911 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7462 (mm) REVERT: C 4992 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8360 (mt) REVERT: D 3955 MET cc_start: 0.7440 (mmm) cc_final: 0.7190 (mmm) REVERT: D 3959 LYS cc_start: 0.6664 (tttp) cc_final: 0.6319 (tttp) REVERT: D 3986 TRP cc_start: 0.8321 (m100) cc_final: 0.8095 (m100) REVERT: D 4042 ARG cc_start: 0.6352 (mtm110) cc_final: 0.5866 (mtm180) REVERT: D 4045 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7249 (m) REVERT: D 4196 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.5735 (tp30) REVERT: D 4209 GLN cc_start: 0.7768 (pt0) cc_final: 0.7480 (pm20) REVERT: D 4212 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: D 4224 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: D 4580 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6408 (t80) REVERT: D 4704 LEU cc_start: 0.8974 (tp) cc_final: 0.8377 (mm) REVERT: D 4736 ARG cc_start: 0.6919 (ttp-110) cc_final: 0.6516 (ttp-110) REVERT: D 4874 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6821 (mmm) REVERT: D 4911 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7460 (mm) REVERT: D 4992 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8360 (mt) outliers start: 65 outliers final: 24 residues processed: 395 average time/residue: 1.2054 time to fit residues: 542.8746 Evaluate side-chains 403 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 348 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4224 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 4785 THR 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 4045 VAL 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 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 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4874 MET 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 4045 VAL 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 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 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4874 MET 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 4045 VAL 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 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 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4874 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21208 Z= 0.177 Angle : 0.556 8.813 28644 Z= 0.273 Chirality : 0.037 0.135 3096 Planarity : 0.004 0.071 3612 Dihedral : 9.162 149.876 2776 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.74 % Favored : 98.10 % Rotamer: Outliers : 2.63 % Allowed : 17.07 % Favored : 80.30 % 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: 2.19 (0.17), residues: 2476 helix: 2.23 (0.12), residues: 1696 sheet: -0.70 (0.47), residues: 112 loop : -0.18 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D5019 HIS 0.003 0.001 HIS B3994 PHE 0.027 0.001 PHE C4922 TYR 0.014 0.001 TYR A4687 ARG 0.012 0.001 ARG B4189 *********************** 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 411 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 352 time to evaluate : 2.235 Fit side-chains REVERT: A 3959 LYS cc_start: 0.6615 (tttp) cc_final: 0.6278 (tttp) REVERT: A 3986 TRP cc_start: 0.8303 (m100) cc_final: 0.8072 (m100) REVERT: A 4042 ARG cc_start: 0.6345 (mtm110) cc_final: 0.5784 (mtm180) REVERT: A 4196 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5962 (tp30) REVERT: A 4209 GLN cc_start: 0.7781 (pt0) cc_final: 0.7491 (pm20) REVERT: A 4212 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 4224 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: A 4580 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6416 (t80) REVERT: A 4704 LEU cc_start: 0.9000 (tp) cc_final: 0.8371 (mm) REVERT: A 4911 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7456 (mm) REVERT: A 4992 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8364 (mt) REVERT: B 3955 MET cc_start: 0.7454 (mmm) cc_final: 0.7207 (mmm) REVERT: B 3986 TRP cc_start: 0.8305 (m100) cc_final: 0.8074 (m100) REVERT: B 4042 ARG cc_start: 0.6346 (mtm110) cc_final: 0.5789 (mtm180) REVERT: B 4196 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.5964 (tp30) REVERT: B 4209 GLN cc_start: 0.7778 (pt0) cc_final: 0.7491 (pm20) REVERT: B 4212 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: B 4224 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7293 (pt0) REVERT: B 4580 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6414 (t80) REVERT: B 4704 LEU cc_start: 0.8998 (tp) cc_final: 0.8369 (mm) REVERT: B 4874 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6835 (mmm) REVERT: B 4911 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7462 (mm) REVERT: B 4992 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8362 (mt) REVERT: C 3955 MET cc_start: 0.7457 (mmm) cc_final: 0.7208 (mmm) REVERT: C 3959 LYS cc_start: 0.6609 (tttp) cc_final: 0.6358 (tttp) REVERT: C 3986 TRP cc_start: 0.8306 (m100) cc_final: 0.8074 (m100) REVERT: C 4042 ARG cc_start: 0.6346 (mtm110) cc_final: 0.5785 (mtm180) REVERT: C 4196 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5967 (tp30) REVERT: C 4209 GLN cc_start: 0.7762 (pt0) cc_final: 0.7484 (pm20) REVERT: C 4212 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: C 4224 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7290 (pt0) REVERT: C 4580 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6417 (t80) REVERT: C 4704 LEU cc_start: 0.8998 (tp) cc_final: 0.8370 (mm) REVERT: C 4874 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6831 (mmm) REVERT: C 4911 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7465 (mm) REVERT: C 4992 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8360 (mt) REVERT: D 3955 MET cc_start: 0.7455 (mmm) cc_final: 0.7204 (mmm) REVERT: D 3959 LYS cc_start: 0.6607 (tttp) cc_final: 0.6357 (tttp) REVERT: D 3986 TRP cc_start: 0.8302 (m100) cc_final: 0.8072 (m100) REVERT: D 4042 ARG cc_start: 0.6348 (mtm110) cc_final: 0.5786 (mtm180) REVERT: D 4196 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5841 (tp30) REVERT: D 4209 GLN cc_start: 0.7782 (pt0) cc_final: 0.7491 (pm20) REVERT: D 4212 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: D 4224 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: D 4580 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.6409 (t80) REVERT: D 4704 LEU cc_start: 0.8997 (tp) cc_final: 0.8370 (mm) REVERT: D 4874 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6607 (mmm) REVERT: D 4911 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7464 (mm) REVERT: D 4992 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8363 (mt) outliers start: 59 outliers final: 24 residues processed: 388 average time/residue: 1.2245 time to fit residues: 539.4490 Evaluate side-chains 403 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 352 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4224 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 4045 VAL 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 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 4874 MET 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 4045 VAL 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 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 4874 MET 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 4045 VAL 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 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 4874 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.0670 chunk 143 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21208 Z= 0.172 Angle : 0.573 8.652 28644 Z= 0.280 Chirality : 0.037 0.135 3096 Planarity : 0.004 0.069 3612 Dihedral : 9.134 149.834 2776 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.70 % Favored : 98.14 % Rotamer: Outliers : 2.81 % Allowed : 16.84 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.17), residues: 2476 helix: 2.27 (0.12), residues: 1696 sheet: -0.70 (0.47), residues: 112 loop : -0.17 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A5019 HIS 0.002 0.001 HIS A3994 PHE 0.029 0.001 PHE C4922 TYR 0.015 0.001 TYR A4687 ARG 0.015 0.001 ARG B4736 ********************** 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 fitting. rotamer outliers: 63 poor density : 353 time to evaluate : 2.338 Fit side-chains REVERT: A 3959 LYS cc_start: 0.6588 (tttp) cc_final: 0.6266 (tttp) REVERT: A 4042 ARG cc_start: 0.6333 (mtm110) cc_final: 0.5773 (mtm180) REVERT: A 4196 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5951 (tp30) REVERT: A 4209 GLN cc_start: 0.7747 (pt0) cc_final: 0.7462 (pm20) REVERT: A 4212 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 4224 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: A 4580 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6413 (t80) REVERT: A 4736 ARG cc_start: 0.6882 (ttp-110) cc_final: 0.6529 (ttp-110) REVERT: A 4911 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7453 (mm) REVERT: A 4992 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8362 (mt) REVERT: B 3955 MET cc_start: 0.7547 (mmm) cc_final: 0.7280 (mmm) REVERT: B 4042 ARG cc_start: 0.6328 (mtm110) cc_final: 0.5773 (mtm180) REVERT: B 4196 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5946 (tp30) REVERT: B 4209 GLN cc_start: 0.7746 (pt0) cc_final: 0.7463 (pm20) REVERT: B 4212 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: B 4224 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: B 4580 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6412 (t80) REVERT: B 4736 ARG cc_start: 0.6884 (ttp-110) cc_final: 0.6531 (ttp-110) REVERT: B 4874 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6629 (mmm) REVERT: B 4911 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7460 (mm) REVERT: B 4992 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8359 (mt) REVERT: C 3955 MET cc_start: 0.7550 (mmm) cc_final: 0.7294 (mmm) REVERT: C 3959 LYS cc_start: 0.6559 (tttp) cc_final: 0.6234 (tttp) REVERT: C 4042 ARG cc_start: 0.6328 (mtm110) cc_final: 0.5770 (mtm180) REVERT: C 4196 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5951 (tp30) REVERT: C 4209 GLN cc_start: 0.7748 (pt0) cc_final: 0.7461 (pm20) REVERT: C 4212 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: C 4224 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: C 4580 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6414 (t80) REVERT: C 4736 ARG cc_start: 0.6881 (ttp-110) cc_final: 0.6527 (ttp-110) REVERT: C 4874 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6625 (mmm) REVERT: C 4911 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7463 (mm) REVERT: C 4992 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8357 (mt) REVERT: D 3955 MET cc_start: 0.7546 (mmm) cc_final: 0.7289 (mmm) REVERT: D 3959 LYS cc_start: 0.6563 (tttp) cc_final: 0.6236 (tttp) REVERT: D 4042 ARG cc_start: 0.6326 (mtm110) cc_final: 0.5770 (mtm180) REVERT: D 4196 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5947 (tp30) REVERT: D 4209 GLN cc_start: 0.7751 (pt0) cc_final: 0.7462 (pm20) REVERT: D 4212 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: D 4224 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7312 (pt0) REVERT: D 4580 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6404 (t80) REVERT: D 4736 ARG cc_start: 0.6876 (ttp-110) cc_final: 0.6522 (ttp-110) REVERT: D 4874 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6568 (mmm) REVERT: D 4911 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7461 (mm) REVERT: D 4992 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8359 (mt) outliers start: 63 outliers final: 28 residues processed: 392 average time/residue: 1.2283 time to fit residues: 548.5808 Evaluate side-chains 390 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 335 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4224 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 4785 THR 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 4045 VAL 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 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 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4874 MET 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 4045 VAL 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 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 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4874 MET 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 4045 VAL 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 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 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4874 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 173 optimal weight: 0.0770 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.176654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142360 restraints weight = 24438.494| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.08 r_work: 0.3348 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21208 Z= 0.188 Angle : 0.576 8.338 28644 Z= 0.283 Chirality : 0.037 0.137 3096 Planarity : 0.004 0.071 3612 Dihedral : 9.153 150.137 2776 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.67 % Allowed : 16.98 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.17), residues: 2476 helix: 2.06 (0.12), residues: 1724 sheet: -0.79 (0.47), residues: 112 loop : -0.08 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3986 HIS 0.003 0.001 HIS D3994 PHE 0.031 0.001 PHE B4922 TYR 0.018 0.001 TYR A4687 ARG 0.015 0.001 ARG B4189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9028.70 seconds wall clock time: 158 minutes 2.72 seconds (9482.72 seconds total)