Starting phenix.real_space_refine on Wed Jun 18 07:24:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sex_40432/06_2025/8sex_40432.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sex_40432/06_2025/8sex_40432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sex_40432/06_2025/8sex_40432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sex_40432/06_2025/8sex_40432.map" model { file = "/net/cci-nas-00/data/ceres_data/8sex_40432/06_2025/8sex_40432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sex_40432/06_2025/8sex_40432.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 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 4 5.49 5 S 160 5.16 5 C 13344 2.51 5 N 3280 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5118 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' ZN': 1, 'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4444 SG CYS A4958 56.003 81.965 85.909 1.00 45.49 S ATOM 4469 SG CYS A4961 58.285 82.520 88.873 1.00 43.92 S Restraints were copied for chains: C, B, D Time building chain proxies: 12.18, per 1000 atoms: 0.59 Number of scatterers: 20568 At special positions: 0 Unit cell: (142.968, 142.968, 130.088, 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 4 15.00 O 3776 8.00 N 3280 7.00 C 13344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.25 Conformation dependent library (CDL) restraints added in 2.5 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 A4958 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " 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 B4958 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " 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 C4958 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " 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 D4958 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " Number of angles added : 8 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4712 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 8 sheets defined 79.6% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 3950 through 3970 removed outlier: 3.871A pdb=" N ALA A3954 " --> pdb=" O ASN A3950 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3983 Processing helix chain 'A' and resid 3984 through 4006 removed outlier: 3.590A pdb=" N ALA A3988 " --> pdb=" O ARG A3984 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4031 removed outlier: 3.800A pdb=" N LEU A4019 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.519A 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 4056 Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4207 through 4224 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4543 through 4558 Processing helix chain 'A' and resid 4558 through 4578 removed outlier: 3.507A pdb=" N LEU A4578 " --> pdb=" O ASN A4574 " (cutoff:3.500A) 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 4702 Processing helix chain 'A' and resid 4702 through 4707 removed outlier: 3.915A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4702 through 4707' Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 5.245A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 Processing helix chain 'A' and resid 4744 through 4749 removed outlier: 3.930A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) Processing helix chain 'A' and resid 4773 through 4785 Processing helix chain 'A' and resid 4786 through 4802 Processing helix chain 'A' and resid 4803 through 4804 No H-bonds generated for 'chain 'A' and resid 4803 through 4804' Processing helix chain 'A' and resid 4805 through 4813 Processing helix chain 'A' and resid 4814 through 4820 removed outlier: 4.173A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.690A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.408A 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 4863 removed outlier: 3.577A pdb=" N TYR A4863 " --> pdb=" O ARG A4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4860 through 4863' Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 4.209A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4900 removed outlier: 3.608A pdb=" N ASP A4899 " --> pdb=" O GLY A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4926 through 4957 Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.895A 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 5037 removed outlier: 5.845A pdb=" N ASP A5034 " --> pdb=" O LYS A5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN A5035 " --> pdb=" O GLN A5031 " (cutoff:3.500A) Processing helix chain 'B' and resid 3951 through 3970 Processing helix chain 'B' and resid 3973 through 3983 Processing helix chain 'B' and resid 3984 through 4006 removed outlier: 3.590A pdb=" N ALA B3988 " --> pdb=" O ARG B3984 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4031 removed outlier: 3.800A pdb=" N LEU B4019 " --> pdb=" O GLU B4015 " (cutoff:3.500A) removed outlier: 3.519A 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 4056 Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4207 through 4224 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4543 through 4558 Processing helix chain 'B' and resid 4558 through 4578 removed outlier: 3.507A pdb=" N LEU B4578 " --> pdb=" O ASN B4574 " (cutoff:3.500A) 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 4702 Processing helix chain 'B' and resid 4702 through 4707 removed outlier: 3.915A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4702 through 4707' Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 5.245A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 Processing helix chain 'B' and resid 4744 through 4749 removed outlier: 3.930A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) Processing helix chain 'B' and resid 4773 through 4785 Processing helix chain 'B' and resid 4786 through 4802 Processing helix chain 'B' and resid 4803 through 4804 No H-bonds generated for 'chain 'B' and resid 4803 through 4804' Processing helix chain 'B' and resid 4805 through 4813 Processing helix chain 'B' and resid 4814 through 4820 removed outlier: 4.173A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.690A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.408A 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 4863 removed outlier: 3.577A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4860 through 4863' Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.209A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4900 removed outlier: 3.608A pdb=" N ASP B4899 " --> pdb=" O GLY B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4926 through 4957 Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 3.895A 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 5037 removed outlier: 5.845A pdb=" N ASP B5034 " --> pdb=" O LYS B5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN B5035 " --> pdb=" O GLN B5031 " (cutoff:3.500A) Processing helix chain 'C' and resid 3951 through 3970 Processing helix chain 'C' and resid 3973 through 3983 Processing helix chain 'C' and resid 3984 through 4006 removed outlier: 3.590A pdb=" N ALA C3988 " --> pdb=" O ARG C3984 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4031 removed outlier: 3.800A pdb=" N LEU C4019 " --> pdb=" O GLU C4015 " (cutoff:3.500A) removed outlier: 3.519A 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 4056 Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4207 through 4224 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4543 through 4558 Processing helix chain 'C' and resid 4558 through 4578 removed outlier: 3.507A pdb=" N LEU C4578 " --> pdb=" O ASN C4574 " (cutoff:3.500A) 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 4702 Processing helix chain 'C' and resid 4702 through 4707 removed outlier: 3.915A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4702 through 4707' Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 5.245A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 Processing helix chain 'C' and resid 4744 through 4749 removed outlier: 3.930A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) Processing helix chain 'C' and resid 4773 through 4785 Processing helix chain 'C' and resid 4786 through 4802 Processing helix chain 'C' and resid 4803 through 4804 No H-bonds generated for 'chain 'C' and resid 4803 through 4804' Processing helix chain 'C' and resid 4805 through 4813 Processing helix chain 'C' and resid 4814 through 4820 removed outlier: 4.173A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.690A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.408A 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 4863 removed outlier: 3.577A pdb=" N TYR C4863 " --> pdb=" O ARG C4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4860 through 4863' Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.209A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4900 removed outlier: 3.608A pdb=" N ASP C4899 " --> pdb=" O GLY C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4926 through 4957 Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 3.895A 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 5037 removed outlier: 5.845A pdb=" N ASP C5034 " --> pdb=" O LYS C5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN C5035 " --> pdb=" O GLN C5031 " (cutoff:3.500A) Processing helix chain 'D' and resid 3951 through 3970 Processing helix chain 'D' and resid 3973 through 3983 Processing helix chain 'D' and resid 3984 through 4006 removed outlier: 3.590A pdb=" N ALA D3988 " --> pdb=" O ARG D3984 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4031 removed outlier: 3.800A pdb=" N LEU D4019 " --> pdb=" O GLU D4015 " (cutoff:3.500A) removed outlier: 3.519A 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 4056 Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4207 through 4224 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4543 through 4558 Processing helix chain 'D' and resid 4558 through 4578 removed outlier: 3.507A pdb=" N LEU D4578 " --> pdb=" O ASN D4574 " (cutoff:3.500A) 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 4702 Processing helix chain 'D' and resid 4702 through 4707 removed outlier: 3.915A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4702 through 4707' Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 5.245A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4744 through 4749 removed outlier: 3.930A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) Processing helix chain 'D' and resid 4773 through 4785 Processing helix chain 'D' and resid 4786 through 4802 Processing helix chain 'D' and resid 4803 through 4804 No H-bonds generated for 'chain 'D' and resid 4803 through 4804' Processing helix chain 'D' and resid 4805 through 4813 Processing helix chain 'D' and resid 4814 through 4820 removed outlier: 4.173A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.690A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.408A 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 4863 removed outlier: 3.577A pdb=" N TYR D4863 " --> pdb=" O ARG D4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4860 through 4863' Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.209A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4900 removed outlier: 3.608A pdb=" N ASP D4899 " --> pdb=" O GLY D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4926 through 4957 Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 3.895A 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 5037 removed outlier: 5.845A pdb=" N ASP D5034 " --> pdb=" O LYS D5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN D5035 " --> pdb=" O GLN D5031 " (cutoff:3.500A) 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 1396 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: 6.71 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6484 1.34 - 1.46: 4196 1.46 - 1.57: 10088 1.57 - 1.69: 4 1.69 - 1.81: 276 Bond restraints: 21048 Sorted by residual: bond pdb=" C4 AMP C5101 " pdb=" C5 AMP C5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 AMP D5101 " pdb=" C5 AMP D5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 AMP A5101 " pdb=" C5 AMP A5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 AMP B5101 " pdb=" C5 AMP B5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C5 AMP A5101 " pdb=" C6 AMP A5101 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 28152 2.29 - 4.58: 200 4.58 - 6.87: 36 6.87 - 9.16: 20 9.16 - 11.44: 8 Bond angle restraints: 28416 Sorted by residual: angle pdb=" C LYS D4665 " pdb=" N VAL D4666 " pdb=" CA VAL D4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C LYS C4665 " pdb=" N VAL C4666 " pdb=" CA VAL C4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C LYS A4665 " pdb=" N VAL A4666 " pdb=" CA VAL A4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C LYS B4665 " pdb=" N VAL B4666 " pdb=" CA VAL B4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C1' AMP D5101 " pdb=" C2' AMP D5101 " pdb=" C3' AMP D5101 " ideal model delta sigma weight residual 111.00 99.56 11.44 3.00e+00 1.11e-01 1.46e+01 ... (remaining 28411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 12100 30.78 - 61.57: 280 61.57 - 92.35: 8 92.35 - 123.13: 0 123.13 - 153.92: 4 Dihedral angle restraints: 12392 sinusoidal: 5080 harmonic: 7312 Sorted by residual: dihedral pdb=" C2' AMP C5101 " pdb=" C1' AMP C5101 " pdb=" N9 AMP C5101 " pdb=" C4 AMP C5101 " ideal model delta sinusoidal sigma weight residual 91.55 -62.36 153.92 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C2' AMP B5101 " pdb=" C1' AMP B5101 " pdb=" N9 AMP B5101 " pdb=" C4 AMP B5101 " ideal model delta sinusoidal sigma weight residual 91.55 -62.36 153.92 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C2' AMP A5101 " pdb=" C1' AMP A5101 " pdb=" N9 AMP A5101 " pdb=" C4 AMP A5101 " ideal model delta sinusoidal sigma weight residual 91.55 -62.36 153.92 1 2.00e+01 2.50e-03 4.56e+01 ... (remaining 12389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2008 0.036 - 0.073: 900 0.073 - 0.109: 140 0.109 - 0.145: 24 0.145 - 0.182: 8 Chirality restraints: 3080 Sorted by residual: chirality pdb=" C3' AMP D5101 " pdb=" C2' AMP D5101 " pdb=" C4' AMP D5101 " pdb=" O3' AMP D5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" C3' AMP C5101 " pdb=" C2' AMP C5101 " pdb=" C4' AMP C5101 " pdb=" O3' AMP C5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" C3' AMP A5101 " pdb=" C2' AMP A5101 " pdb=" C4' AMP A5101 " pdb=" O3' AMP A5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 3077 not shown) Planarity restraints: 3592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A3971 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO A3972 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO A3972 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A3972 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B3971 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO B3972 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO B3972 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO B3972 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C3971 " -0.083 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO C3972 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO C3972 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO C3972 " -0.065 5.00e-02 4.00e+02 ... (remaining 3589 not shown) Histogram of nonbonded interaction distances: 0.42 - 1.31: 16 1.31 - 2.21: 28 2.21 - 3.11: 15256 3.11 - 4.00: 54528 4.00 - 4.90: 101440 Warning: very small nonbonded interaction distances. Nonbonded interactions: 171268 Sorted by model distance: nonbonded pdb=" NH2 ARG A4944 " pdb=" OD1 ASP B4938 " model vdw 0.419 3.120 nonbonded pdb=" NH2 ARG B4944 " pdb=" OD1 ASP C4938 " model vdw 0.419 3.120 nonbonded pdb=" OD1 ASP A4938 " pdb=" NH2 ARG D4944 " model vdw 0.419 3.120 nonbonded pdb=" NH2 ARG C4944 " pdb=" OD1 ASP D4938 " model vdw 0.419 3.120 nonbonded pdb=" NH2 ARG A4944 " pdb=" CG ASP B4938 " model vdw 1.035 3.350 ... (remaining 171263 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 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: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 49.730 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.005 0.110 21068 Z= 0.230 Angle : 0.605 11.445 28432 Z= 0.300 Chirality : 0.039 0.182 3080 Planarity : 0.005 0.126 3592 Dihedral : 12.773 153.916 7668 Min Nonbonded Distance : 0.419 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.76 % Favored : 97.08 % Rotamer: Outliers : 2.15 % Allowed : 6.45 % Favored : 91.40 % 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: 1.60 (0.17), residues: 2464 helix: 1.56 (0.12), residues: 1664 sheet: -0.11 (0.54), residues: 104 loop : 0.20 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A4716 HIS 0.003 0.001 HIS C4650 PHE 0.020 0.002 PHE D4916 TYR 0.017 0.002 TYR D4994 ARG 0.002 0.001 ARG D4673 Details of bonding type rmsd hydrogen bonds : bond 0.15115 ( 1396) hydrogen bonds : angle 5.18237 ( 4068) metal coordination : bond 0.00711 ( 16) metal coordination : angle 7.00607 ( 8) SS BOND : bond 0.00093 ( 4) SS BOND : angle 1.26743 ( 8) covalent geometry : bond 0.00521 (21048) covalent geometry : angle 0.59281 (28416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 392 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4047 MET cc_start: 0.6927 (tmm) cc_final: 0.6382 (tmm) REVERT: A 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6265 (t80) REVERT: A 4629 TYR cc_start: 0.7423 (m-80) cc_final: 0.7091 (m-80) REVERT: A 4698 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7719 (ttmm) REVERT: A 4949 GLN cc_start: 0.8113 (tp40) cc_final: 0.7646 (mp10) REVERT: A 5006 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7462 (pt0) REVERT: A 5030 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7527 (ttpt) REVERT: B 4047 MET cc_start: 0.6926 (tmm) cc_final: 0.6382 (tmm) REVERT: B 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6263 (t80) REVERT: B 4629 TYR cc_start: 0.7419 (m-80) cc_final: 0.7089 (m-80) REVERT: B 4698 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7722 (ttmm) REVERT: B 4949 GLN cc_start: 0.8112 (tp40) cc_final: 0.7646 (mp10) REVERT: B 5006 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: B 5030 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7532 (ttpt) REVERT: C 4047 MET cc_start: 0.6927 (tmm) cc_final: 0.6380 (tmm) REVERT: C 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6269 (t80) REVERT: C 4629 TYR cc_start: 0.7422 (m-80) cc_final: 0.7093 (m-80) REVERT: C 4698 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7719 (ttmm) REVERT: C 4949 GLN cc_start: 0.8110 (tp40) cc_final: 0.7646 (mp10) REVERT: C 5006 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7458 (pt0) REVERT: C 5030 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7528 (ttpt) REVERT: D 4047 MET cc_start: 0.6924 (tmm) cc_final: 0.6380 (tmm) REVERT: D 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6266 (t80) REVERT: D 4629 TYR cc_start: 0.7426 (m-80) cc_final: 0.7094 (m-80) REVERT: D 4698 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7720 (ttmm) REVERT: D 4949 GLN cc_start: 0.8113 (tp40) cc_final: 0.7649 (mp10) REVERT: D 5006 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: D 5030 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7528 (ttpt) outliers start: 48 outliers final: 24 residues processed: 436 average time/residue: 1.3552 time to fit residues: 665.9604 Evaluate side-chains 332 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4027 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4027 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4027 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 225 optimal weight: 0.0020 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3963 ASN A3978 GLN A4020 GLN A4997 ASN B3963 ASN B3978 GLN B4020 GLN B4997 ASN C3963 ASN C3978 GLN C4020 GLN C4997 ASN D3963 ASN D3978 GLN D4020 GLN D4997 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.178653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.143166 restraints weight = 23359.320| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.40 r_work: 0.3277 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21068 Z= 0.136 Angle : 0.550 7.752 28432 Z= 0.283 Chirality : 0.038 0.173 3080 Planarity : 0.006 0.124 3592 Dihedral : 8.136 153.142 2784 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.60 % Favored : 97.24 % Rotamer: Outliers : 3.41 % Allowed : 11.65 % Favored : 84.95 % 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: 2464 helix: 2.07 (0.12), residues: 1684 sheet: -0.55 (0.50), residues: 104 loop : 0.18 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A4716 HIS 0.004 0.001 HIS D4973 PHE 0.017 0.001 PHE C4916 TYR 0.014 0.001 TYR D4687 ARG 0.006 0.001 ARG C4188 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 1396) hydrogen bonds : angle 4.25402 ( 4068) metal coordination : bond 0.00630 ( 16) metal coordination : angle 4.58065 ( 8) SS BOND : bond 0.00054 ( 4) SS BOND : angle 1.12382 ( 8) covalent geometry : bond 0.00305 (21048) covalent geometry : angle 0.54476 (28416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 336 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4022 ASP cc_start: 0.6965 (m-30) cc_final: 0.6623 (m-30) REVERT: A 4047 MET cc_start: 0.6535 (tmm) cc_final: 0.5810 (tmm) REVERT: A 4196 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.3954 (tp30) REVERT: A 4580 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.6695 (t80) REVERT: A 4933 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7626 (mt0) REVERT: A 4949 GLN cc_start: 0.8610 (tp40) cc_final: 0.7955 (mp10) REVERT: A 4956 THR cc_start: 0.8793 (p) cc_final: 0.8491 (p) REVERT: A 5030 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7904 (ttmt) REVERT: A 5032 TYR cc_start: 0.8024 (m-80) cc_final: 0.7236 (m-80) REVERT: B 4022 ASP cc_start: 0.6940 (m-30) cc_final: 0.6571 (m-30) REVERT: B 4047 MET cc_start: 0.6525 (tmm) cc_final: 0.5800 (tmm) REVERT: B 4196 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.3943 (tp30) REVERT: B 4580 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.6700 (t80) REVERT: B 4933 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: B 4949 GLN cc_start: 0.8596 (tp40) cc_final: 0.7952 (mp10) REVERT: B 4956 THR cc_start: 0.8792 (p) cc_final: 0.8492 (p) REVERT: B 5030 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7922 (ttmt) REVERT: B 5032 TYR cc_start: 0.8040 (m-80) cc_final: 0.7261 (m-80) REVERT: C 4022 ASP cc_start: 0.6933 (m-30) cc_final: 0.6567 (m-30) REVERT: C 4047 MET cc_start: 0.6526 (tmm) cc_final: 0.5803 (tmm) REVERT: C 4196 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.3930 (tp30) REVERT: C 4580 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.6695 (t80) REVERT: C 4933 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: C 4949 GLN cc_start: 0.8598 (tp40) cc_final: 0.7938 (mp10) REVERT: C 4956 THR cc_start: 0.8789 (p) cc_final: 0.8488 (p) REVERT: C 5030 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7920 (ttmt) REVERT: C 5032 TYR cc_start: 0.8049 (m-80) cc_final: 0.7262 (m-80) REVERT: D 4022 ASP cc_start: 0.6948 (m-30) cc_final: 0.6579 (m-30) REVERT: D 4047 MET cc_start: 0.6532 (tmm) cc_final: 0.5807 (tmm) REVERT: D 4196 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.3960 (tp30) REVERT: D 4580 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.6677 (t80) REVERT: D 4933 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: D 4949 GLN cc_start: 0.8618 (tp40) cc_final: 0.7938 (mp10) REVERT: D 4956 THR cc_start: 0.8794 (p) cc_final: 0.8491 (p) REVERT: D 5030 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7923 (ttmt) REVERT: D 5032 TYR cc_start: 0.8043 (m-80) cc_final: 0.7257 (m-80) outliers start: 76 outliers final: 28 residues processed: 380 average time/residue: 1.3248 time to fit residues: 569.8436 Evaluate side-chains 344 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4951 LYS Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4951 LYS Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4951 LYS Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4951 LYS Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 119 optimal weight: 0.0970 chunk 177 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.177461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.141740 restraints weight = 23289.110| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.36 r_work: 0.3279 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21068 Z= 0.159 Angle : 0.543 7.663 28432 Z= 0.275 Chirality : 0.038 0.177 3080 Planarity : 0.005 0.122 3592 Dihedral : 7.697 152.529 2748 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.35 % Favored : 97.48 % Rotamer: Outliers : 4.30 % Allowed : 13.44 % Favored : 82.26 % 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: 2464 helix: 2.13 (0.12), residues: 1680 sheet: -0.86 (0.48), residues: 104 loop : 0.06 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C5011 HIS 0.003 0.001 HIS A4803 PHE 0.018 0.002 PHE B4916 TYR 0.014 0.001 TYR A4994 ARG 0.008 0.001 ARG B4042 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 1396) hydrogen bonds : angle 4.21157 ( 4068) metal coordination : bond 0.00864 ( 16) metal coordination : angle 4.93267 ( 8) SS BOND : bond 0.00010 ( 4) SS BOND : angle 1.42778 ( 8) covalent geometry : bond 0.00376 (21048) covalent geometry : angle 0.53678 (28416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 312 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4022 ASP cc_start: 0.6681 (m-30) cc_final: 0.6469 (m-30) REVERT: A 4047 MET cc_start: 0.6613 (tmm) cc_final: 0.5914 (tmm) REVERT: A 4188 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7150 (tpt170) REVERT: A 4580 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.6651 (t80) REVERT: A 4821 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7733 (mmtp) REVERT: A 4844 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8403 (tp) REVERT: A 4933 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: A 4949 GLN cc_start: 0.8490 (tp40) cc_final: 0.7462 (mp10) REVERT: B 4022 ASP cc_start: 0.6671 (m-30) cc_final: 0.6459 (m-30) REVERT: B 4047 MET cc_start: 0.6620 (tmm) cc_final: 0.5919 (tmm) REVERT: B 4188 ARG cc_start: 0.7961 (mmm160) cc_final: 0.7136 (tpt170) REVERT: B 4580 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.6654 (t80) REVERT: B 4821 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7727 (mmtp) REVERT: B 4844 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8404 (tp) REVERT: B 4933 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: B 4949 GLN cc_start: 0.8473 (tp40) cc_final: 0.7445 (mp10) REVERT: C 4022 ASP cc_start: 0.6676 (m-30) cc_final: 0.6463 (m-30) REVERT: C 4047 MET cc_start: 0.6620 (tmm) cc_final: 0.5920 (tmm) REVERT: C 4188 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7133 (tpt170) REVERT: C 4580 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.6656 (t80) REVERT: C 4821 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7720 (mmtp) REVERT: C 4844 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8408 (tp) REVERT: C 4933 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: C 4949 GLN cc_start: 0.8471 (tp40) cc_final: 0.7438 (mp10) REVERT: D 4022 ASP cc_start: 0.6693 (m-30) cc_final: 0.6483 (m-30) REVERT: D 4047 MET cc_start: 0.6614 (tmm) cc_final: 0.5912 (tmm) REVERT: D 4188 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7147 (tpt170) REVERT: D 4580 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.6638 (t80) REVERT: D 4821 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7732 (mmtp) REVERT: D 4844 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8399 (tp) REVERT: D 4933 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: D 4949 GLN cc_start: 0.8484 (tp40) cc_final: 0.7445 (mp10) outliers start: 96 outliers final: 40 residues processed: 376 average time/residue: 1.2684 time to fit residues: 541.3808 Evaluate side-chains 348 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4951 LYS Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4951 LYS Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4951 LYS Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4951 LYS Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 212 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 231 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3963 ASN A3998 HIS ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3998 HIS ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3998 HIS ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.178955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143142 restraints weight = 23652.990| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.95 r_work: 0.3269 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21068 Z= 0.128 Angle : 0.516 6.971 28432 Z= 0.261 Chirality : 0.037 0.175 3080 Planarity : 0.005 0.118 3592 Dihedral : 7.540 150.609 2748 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.56 % Rotamer: Outliers : 3.72 % Allowed : 14.02 % Favored : 82.26 % 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: 2464 helix: 2.33 (0.12), residues: 1680 sheet: -1.05 (0.49), residues: 104 loop : 0.04 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C4716 HIS 0.002 0.001 HIS A3998 PHE 0.016 0.001 PHE C4916 TYR 0.013 0.001 TYR C4687 ARG 0.005 0.001 ARG B4189 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 1396) hydrogen bonds : angle 4.12079 ( 4068) metal coordination : bond 0.00441 ( 16) metal coordination : angle 4.35951 ( 8) SS BOND : bond 0.00024 ( 4) SS BOND : angle 1.17363 ( 8) covalent geometry : bond 0.00298 (21048) covalent geometry : angle 0.51069 (28416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 316 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4047 MET cc_start: 0.6498 (tmm) cc_final: 0.5818 (tmm) REVERT: A 4188 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7296 (tpt170) REVERT: A 4551 PHE cc_start: 0.7658 (t80) cc_final: 0.7431 (t80) REVERT: A 4580 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.6725 (t80) REVERT: A 4697 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7773 (t) REVERT: A 4844 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8500 (tp) REVERT: A 4933 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: A 4949 GLN cc_start: 0.8570 (tp40) cc_final: 0.7598 (mp10) REVERT: A 5006 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7508 (pt0) REVERT: A 5032 TYR cc_start: 0.7990 (m-80) cc_final: 0.7706 (m-80) REVERT: B 4022 ASP cc_start: 0.6644 (m-30) cc_final: 0.6397 (m-30) REVERT: B 4047 MET cc_start: 0.6509 (tmm) cc_final: 0.5829 (tmm) REVERT: B 4188 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7287 (tpt170) REVERT: B 4551 PHE cc_start: 0.7673 (t80) cc_final: 0.7437 (t80) REVERT: B 4580 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.6713 (t80) REVERT: B 4697 VAL cc_start: 0.8007 (OUTLIER) cc_final: 0.7778 (t) REVERT: B 4821 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8063 (mmmt) REVERT: B 4844 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8495 (tp) REVERT: B 4933 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: B 4949 GLN cc_start: 0.8560 (tp40) cc_final: 0.7592 (mp10) REVERT: B 5006 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: B 5032 TYR cc_start: 0.7980 (m-80) cc_final: 0.7702 (m-80) REVERT: C 4022 ASP cc_start: 0.6658 (m-30) cc_final: 0.6414 (m-30) REVERT: C 4047 MET cc_start: 0.6511 (tmm) cc_final: 0.5831 (tmm) REVERT: C 4188 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7284 (tpt170) REVERT: C 4551 PHE cc_start: 0.7648 (t80) cc_final: 0.7423 (t80) REVERT: C 4580 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.6717 (t80) REVERT: C 4697 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7770 (t) REVERT: C 4821 LYS cc_start: 0.8276 (mmtt) cc_final: 0.8062 (mmmt) REVERT: C 4844 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8501 (tp) REVERT: C 4933 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: C 4949 GLN cc_start: 0.8554 (tp40) cc_final: 0.7585 (mp10) REVERT: C 5006 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7508 (pt0) REVERT: C 5032 TYR cc_start: 0.7984 (m-80) cc_final: 0.7705 (m-80) REVERT: D 4022 ASP cc_start: 0.6674 (m-30) cc_final: 0.6427 (m-30) REVERT: D 4047 MET cc_start: 0.6507 (tmm) cc_final: 0.5824 (tmm) REVERT: D 4188 ARG cc_start: 0.8068 (mmm160) cc_final: 0.7296 (tpt170) REVERT: D 4551 PHE cc_start: 0.7648 (t80) cc_final: 0.7429 (t80) REVERT: D 4580 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.6711 (t80) REVERT: D 4697 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7765 (t) REVERT: D 4821 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8067 (mmmt) REVERT: D 4844 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8499 (tp) REVERT: D 4933 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: D 4949 GLN cc_start: 0.8569 (tp40) cc_final: 0.7584 (mp10) REVERT: D 5006 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: D 5032 TYR cc_start: 0.7996 (m-80) cc_final: 0.7712 (m-80) outliers start: 83 outliers final: 40 residues processed: 375 average time/residue: 1.3104 time to fit residues: 557.0789 Evaluate side-chains 359 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 299 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4676 GLU Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4951 LYS Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4676 GLU Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4951 LYS Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4676 GLU Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4951 LYS Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4951 LYS Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5006 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 205 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 183 optimal weight: 0.2980 chunk 117 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 85 optimal weight: 0.0870 chunk 130 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3963 ASN ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3998 HIS ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3963 ASN ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.179780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142130 restraints weight = 23584.226| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.94 r_work: 0.3244 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 0.066 21068 Z= 0.113 Angle : 0.493 6.424 28432 Z= 0.249 Chirality : 0.036 0.178 3080 Planarity : 0.005 0.114 3592 Dihedral : 7.372 148.174 2748 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.56 % Rotamer: Outliers : 4.39 % Allowed : 14.07 % Favored : 81.54 % 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: 2.50 (0.17), residues: 2464 helix: 2.46 (0.12), residues: 1680 sheet: -1.13 (0.49), residues: 104 loop : 0.09 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C5011 HIS 0.002 0.001 HIS B3998 PHE 0.015 0.001 PHE D4916 TYR 0.012 0.001 TYR B4687 ARG 0.006 0.000 ARG D4189 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 1396) hydrogen bonds : angle 4.04077 ( 4068) metal coordination : bond 0.00178 ( 16) metal coordination : angle 3.88801 ( 8) SS BOND : bond 0.00031 ( 4) SS BOND : angle 1.05041 ( 8) covalent geometry : bond 0.00260 (21048) covalent geometry : angle 0.48859 (28416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 311 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4020 GLN cc_start: 0.7006 (tt0) cc_final: 0.6725 (tp40) REVERT: A 4047 MET cc_start: 0.6419 (tmm) cc_final: 0.5773 (tmm) REVERT: A 4188 ARG cc_start: 0.7949 (mmm160) cc_final: 0.7222 (tpt170) REVERT: A 4207 MET cc_start: 0.8447 (mmm) cc_final: 0.8214 (mtp) REVERT: A 4580 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.6549 (t80) REVERT: A 4697 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7860 (t) REVERT: A 4725 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6380 (tp) REVERT: A 4735 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6519 (pm20) REVERT: A 4844 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8443 (tp) REVERT: A 4933 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: A 4949 GLN cc_start: 0.8459 (tp40) cc_final: 0.7567 (mp10) REVERT: A 5006 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: A 5032 TYR cc_start: 0.8029 (m-80) cc_final: 0.7617 (m-80) REVERT: B 3959 LYS cc_start: 0.6209 (OUTLIER) cc_final: 0.5832 (tttp) REVERT: B 4020 GLN cc_start: 0.7144 (tt0) cc_final: 0.6874 (tp40) REVERT: B 4047 MET cc_start: 0.6422 (tmm) cc_final: 0.5772 (tmm) REVERT: B 4188 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7215 (tpt170) REVERT: B 4207 MET cc_start: 0.8453 (mmm) cc_final: 0.8220 (mtp) REVERT: B 4580 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.6544 (t80) REVERT: B 4697 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7874 (t) REVERT: B 4725 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6371 (tp) REVERT: B 4735 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6510 (pm20) REVERT: B 4821 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7950 (mmmm) REVERT: B 4844 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8445 (tp) REVERT: B 4933 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: B 4949 GLN cc_start: 0.8444 (tp40) cc_final: 0.7562 (mp10) REVERT: B 4956 THR cc_start: 0.8809 (p) cc_final: 0.8599 (p) REVERT: B 5006 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: B 5032 TYR cc_start: 0.8032 (m-80) cc_final: 0.7622 (m-80) REVERT: C 4020 GLN cc_start: 0.7149 (tt0) cc_final: 0.6879 (tp40) REVERT: C 4047 MET cc_start: 0.6419 (tmm) cc_final: 0.5776 (tmm) REVERT: C 4188 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7211 (tpt170) REVERT: C 4207 MET cc_start: 0.8457 (mmm) cc_final: 0.8225 (mtp) REVERT: C 4580 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.6544 (t80) REVERT: C 4697 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7863 (t) REVERT: C 4725 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6368 (tp) REVERT: C 4735 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6514 (pm20) REVERT: C 4821 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7954 (mmmm) REVERT: C 4844 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8450 (tp) REVERT: C 4933 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: C 4949 GLN cc_start: 0.8442 (tp40) cc_final: 0.7551 (mp10) REVERT: C 4956 THR cc_start: 0.8803 (p) cc_final: 0.8591 (p) REVERT: C 5006 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7428 (pt0) REVERT: C 5032 TYR cc_start: 0.8041 (m-80) cc_final: 0.7630 (m-80) REVERT: D 3959 LYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5840 (tttp) REVERT: D 4020 GLN cc_start: 0.7143 (tt0) cc_final: 0.6876 (tp40) REVERT: D 4047 MET cc_start: 0.6414 (tmm) cc_final: 0.5765 (tmm) REVERT: D 4188 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7219 (tpt170) REVERT: D 4207 MET cc_start: 0.8447 (mmm) cc_final: 0.8215 (mtp) REVERT: D 4580 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.6561 (t80) REVERT: D 4697 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7861 (t) REVERT: D 4725 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6351 (tp) REVERT: D 4735 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6511 (pm20) REVERT: D 4821 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7953 (mmmm) REVERT: D 4844 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8447 (tp) REVERT: D 4933 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: D 4949 GLN cc_start: 0.8442 (tp40) cc_final: 0.7549 (mp10) REVERT: D 5006 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: D 5032 TYR cc_start: 0.8042 (m-80) cc_final: 0.7628 (m-80) outliers start: 98 outliers final: 28 residues processed: 385 average time/residue: 1.1894 time to fit residues: 522.8153 Evaluate side-chains 347 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 293 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain B residue 3959 LYS Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain D residue 3959 LYS Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5006 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 36 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 169 optimal weight: 0.0670 chunk 176 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5031 GLN B5031 GLN C3963 ASN C5031 GLN D5031 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.178259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141430 restraints weight = 23564.037| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.40 r_work: 0.3295 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21068 Z= 0.146 Angle : 0.524 6.395 28432 Z= 0.265 Chirality : 0.037 0.179 3080 Planarity : 0.005 0.112 3592 Dihedral : 7.371 147.021 2748 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.95 % Favored : 97.89 % Rotamer: Outliers : 4.39 % Allowed : 15.19 % Favored : 80.42 % 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: 2.37 (0.17), residues: 2464 helix: 2.35 (0.12), residues: 1680 sheet: -1.17 (0.48), residues: 104 loop : 0.06 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B5011 HIS 0.003 0.001 HIS B4803 PHE 0.017 0.001 PHE B4916 TYR 0.013 0.001 TYR B4994 ARG 0.007 0.001 ARG B4189 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 1396) hydrogen bonds : angle 4.12766 ( 4068) metal coordination : bond 0.00564 ( 16) metal coordination : angle 4.13259 ( 8) SS BOND : bond 0.00016 ( 4) SS BOND : angle 1.37481 ( 8) covalent geometry : bond 0.00350 (21048) covalent geometry : angle 0.51910 (28416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 315 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4047 MET cc_start: 0.6418 (tmm) cc_final: 0.5782 (tmm) REVERT: A 4188 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7260 (tpt170) REVERT: A 4207 MET cc_start: 0.8267 (mmm) cc_final: 0.7983 (mtp) REVERT: A 4231 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8002 (mmm) REVERT: A 4580 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.6576 (t80) REVERT: A 4725 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6479 (tp) REVERT: A 4844 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8403 (tp) REVERT: A 4933 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: A 4949 GLN cc_start: 0.8457 (tp40) cc_final: 0.7423 (mp10) REVERT: A 5006 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7418 (pt0) REVERT: A 5032 TYR cc_start: 0.7950 (m-80) cc_final: 0.7662 (m-80) REVERT: B 4020 GLN cc_start: 0.7020 (tt0) cc_final: 0.6721 (tp40) REVERT: B 4047 MET cc_start: 0.6412 (tmm) cc_final: 0.5756 (tmm) REVERT: B 4188 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7258 (tpt170) REVERT: B 4207 MET cc_start: 0.8266 (mmm) cc_final: 0.7982 (mtp) REVERT: B 4231 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7999 (mmm) REVERT: B 4580 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.6579 (t80) REVERT: B 4725 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6463 (tp) REVERT: B 4821 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7983 (mmmt) REVERT: B 4844 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8411 (tp) REVERT: B 4933 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: B 4949 GLN cc_start: 0.8435 (tp40) cc_final: 0.7402 (mp10) REVERT: B 4956 THR cc_start: 0.8811 (p) cc_final: 0.8599 (p) REVERT: B 5006 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: B 5032 TYR cc_start: 0.7945 (m-80) cc_final: 0.7663 (m-80) REVERT: C 3959 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.6056 (tttm) REVERT: C 4047 MET cc_start: 0.6413 (tmm) cc_final: 0.5761 (tmm) REVERT: C 4188 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7259 (tpt170) REVERT: C 4207 MET cc_start: 0.8277 (mmm) cc_final: 0.7993 (mtp) REVERT: C 4231 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8000 (mmm) REVERT: C 4580 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.6573 (t80) REVERT: C 4697 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7712 (t) REVERT: C 4725 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6464 (tp) REVERT: C 4821 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7983 (mmmt) REVERT: C 4844 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8408 (tp) REVERT: C 4933 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: C 4949 GLN cc_start: 0.8436 (tp40) cc_final: 0.7391 (mp10) REVERT: C 4956 THR cc_start: 0.8801 (p) cc_final: 0.8588 (p) REVERT: C 5006 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: C 5032 TYR cc_start: 0.7946 (m-80) cc_final: 0.7663 (m-80) REVERT: D 4020 GLN cc_start: 0.7025 (tt0) cc_final: 0.6725 (tp40) REVERT: D 4047 MET cc_start: 0.6412 (tmm) cc_final: 0.5755 (tmm) REVERT: D 4188 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7262 (tpt170) REVERT: D 4207 MET cc_start: 0.8275 (mmm) cc_final: 0.7992 (mtp) REVERT: D 4231 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7995 (mmm) REVERT: D 4580 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.6561 (t80) REVERT: D 4697 VAL cc_start: 0.7920 (OUTLIER) cc_final: 0.7717 (t) REVERT: D 4725 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6463 (tp) REVERT: D 4821 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7981 (mmmt) REVERT: D 4844 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8404 (tp) REVERT: D 4933 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: D 4949 GLN cc_start: 0.8449 (tp40) cc_final: 0.7400 (mp10) REVERT: D 5006 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: D 5032 TYR cc_start: 0.7951 (m-80) cc_final: 0.7662 (m-80) outliers start: 98 outliers final: 40 residues processed: 381 average time/residue: 1.2282 time to fit residues: 531.8948 Evaluate side-chains 358 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 291 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4231 MET Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4231 MET Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain C residue 3959 LYS Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4231 MET Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4231 MET Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5006 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9956 > 50: distance: 47 - 68: 26.860 distance: 52 - 76: 34.011 distance: 64 - 68: 28.659 distance: 68 - 69: 4.736 distance: 69 - 70: 24.600 distance: 69 - 72: 21.015 distance: 70 - 71: 16.120 distance: 70 - 76: 27.397 distance: 72 - 73: 28.628 distance: 73 - 74: 20.120 distance: 73 - 75: 21.789 distance: 76 - 77: 49.214 distance: 77 - 78: 10.933 distance: 78 - 79: 21.603 distance: 78 - 80: 37.688 distance: 80 - 81: 11.942 distance: 81 - 82: 24.454 distance: 81 - 84: 12.100 distance: 82 - 90: 23.749 distance: 84 - 85: 28.202 distance: 85 - 86: 14.349 distance: 85 - 87: 28.310 distance: 86 - 88: 30.785 distance: 88 - 89: 15.782 distance: 90 - 91: 10.313 distance: 91 - 92: 19.832 distance: 91 - 94: 18.863 distance: 92 - 93: 13.509 distance: 92 - 102: 20.275 distance: 94 - 95: 22.926 distance: 95 - 96: 15.231 distance: 95 - 97: 22.700 distance: 96 - 98: 20.416 distance: 97 - 99: 19.582 distance: 98 - 100: 34.005 distance: 99 - 100: 16.903 distance: 100 - 101: 15.824 distance: 102 - 103: 13.164 distance: 103 - 104: 22.295 distance: 103 - 106: 24.165 distance: 104 - 105: 48.815 distance: 104 - 110: 20.465 distance: 105 - 129: 59.380 distance: 106 - 107: 46.394 distance: 107 - 108: 18.691 distance: 107 - 109: 28.167 distance: 110 - 111: 27.946 distance: 111 - 112: 16.583 distance: 111 - 114: 30.662 distance: 112 - 113: 40.231 distance: 112 - 118: 11.098 distance: 113 - 140: 35.698 distance: 114 - 115: 30.886 distance: 115 - 116: 27.082 distance: 115 - 117: 41.421 distance: 118 - 119: 21.597 distance: 119 - 120: 31.840 distance: 119 - 122: 7.879 distance: 120 - 121: 13.351 distance: 120 - 129: 29.541 distance: 121 - 151: 44.609 distance: 122 - 123: 12.989 distance: 123 - 124: 19.363 distance: 123 - 125: 14.326 distance: 124 - 126: 26.324 distance: 125 - 127: 26.483 distance: 126 - 128: 14.685 distance: 127 - 128: 30.526 distance: 129 - 130: 24.902 distance: 130 - 131: 30.378 distance: 130 - 133: 34.381 distance: 131 - 132: 52.550 distance: 131 - 140: 7.408 distance: 132 - 156: 27.273 distance: 133 - 134: 29.864 distance: 134 - 135: 26.638 distance: 134 - 136: 13.729 distance: 135 - 137: 12.104 distance: 136 - 138: 17.487 distance: 138 - 139: 16.071 distance: 140 - 141: 27.052 distance: 141 - 142: 31.570 distance: 141 - 144: 20.374 distance: 142 - 143: 58.727 distance: 142 - 151: 7.379 distance: 143 - 161: 30.067 distance: 144 - 145: 12.443 distance: 145 - 146: 32.707 distance: 145 - 147: 15.442 distance: 146 - 148: 11.944 distance: 147 - 149: 41.774 distance: 148 - 150: 32.475 distance: 149 - 150: 31.413 distance: 151 - 152: 24.712 distance: 152 - 153: 3.038 distance: 152 - 155: 23.524 distance: 153 - 154: 9.874 distance: 153 - 156: 10.938 distance: 154 - 170: 15.405