Starting phenix.real_space_refine on Wed Nov 20 05:22:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/11_2024/8sev_40430.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/11_2024/8sev_40430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/11_2024/8sev_40430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/11_2024/8sev_40430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/11_2024/8sev_40430.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/11_2024/8sev_40430.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.123 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 12 5.49 5 S 164 5.16 5 C 13380 2.51 5 N 3284 2.21 5 O 3788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20632 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5126 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "B" Number of atoms: 5126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5126 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "C" Number of atoms: 5126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5126 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "D" Number of atoms: 5126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5126 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4452 SG CYS A4958 57.043 82.993 88.700 1.00 62.76 S ATOM 4477 SG CYS A4961 59.631 83.670 91.460 1.00 61.89 S ATOM 9578 SG CYS B4958 61.263 57.043 88.700 1.00 63.22 S ATOM 9603 SG CYS B4961 60.585 59.630 91.460 1.00 62.33 S ATOM 14704 SG CYS C4958 87.213 61.263 88.700 1.00 64.07 S ATOM 14729 SG CYS C4961 84.625 60.585 91.459 1.00 63.16 S ATOM 19830 SG CYS D4958 82.993 87.213 88.700 1.00 64.33 S ATOM 19855 SG CYS D4961 83.670 84.625 91.460 1.00 63.21 S Time building chain proxies: 12.14, per 1000 atoms: 0.59 Number of scatterers: 20632 At special positions: 0 Unit cell: (145.544, 145.544, 133.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 164 16.00 P 12 15.00 O 3788 8.00 N 3284 7.00 C 13380 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 B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " 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: 5.35 Conformation dependent library (CDL) restraints added in 2.8 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 B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 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: 136 helices and 8 sheets defined 77.7% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 3950 through 3970 removed outlier: 4.521A pdb=" N ALA A3954 " --> pdb=" O ASN A3950 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3982 Processing helix chain 'A' and resid 3984 through 3990 Processing helix chain 'A' and resid 3992 through 4006 removed outlier: 4.051A pdb=" N MET A4000 " --> pdb=" O PHE A3996 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4031 Processing helix chain 'A' and resid 4038 through 4051 removed outlier: 3.634A pdb=" N VAL A4045 " --> pdb=" O ALA A4041 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A4046 " --> pdb=" O ARG A4042 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4060 Processing helix chain 'A' and resid 4198 through 4206 Processing helix chain 'A' and resid 4207 through 4224 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4541 through 4558 removed outlier: 3.771A pdb=" N VAL A4546 " --> pdb=" O GLY A4542 " (cutoff:3.500A) Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4665 removed outlier: 3.572A pdb=" N LEU A4652 " --> pdb=" O LEU A4648 " (cutoff:3.500A) Processing helix chain 'A' and resid 4665 through 4683 removed outlier: 3.504A pdb=" N VAL A4669 " --> pdb=" O LYS A4665 " (cutoff:3.500A) Processing helix chain 'A' and resid 4696 through 4703 Processing helix chain 'A' and resid 4704 through 4706 No H-bonds generated for 'chain 'A' and resid 4704 through 4706' Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 5.068A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4734 through 4742 Processing helix chain 'A' and resid 4773 through 4786 removed outlier: 3.501A pdb=" N ASP A4786 " --> pdb=" O VAL A4782 " (cutoff:3.500A) Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.975A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4813 Processing helix chain 'A' and resid 4814 through 4820 removed outlier: 4.012A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.806A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.349A 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 4878 through 4893 removed outlier: 4.334A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4925 removed outlier: 3.587A pdb=" N VAL A4915 " --> pdb=" O LEU A4911 " (cutoff:3.500A) Processing helix chain 'A' and resid 4926 through 4957 removed outlier: 4.586A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A4933 " --> pdb=" O LEU A4929 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.934A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 4999 through 5003 Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5032 Processing helix chain 'A' and resid 5032 through 5037 Processing helix chain 'B' and resid 3951 through 3970 removed outlier: 3.513A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3982 Processing helix chain 'B' and resid 3984 through 3990 Processing helix chain 'B' and resid 3992 through 4006 removed outlier: 4.051A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4031 Processing helix chain 'B' and resid 4038 through 4051 removed outlier: 3.634A pdb=" N VAL B4045 " --> pdb=" O ALA B4041 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B4046 " --> pdb=" O ARG B4042 " (cutoff:3.500A) Processing helix chain 'B' and resid 4051 through 4060 Processing helix chain 'B' and resid 4198 through 4206 Processing helix chain 'B' and resid 4207 through 4224 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4541 through 4558 removed outlier: 3.771A pdb=" N VAL B4546 " --> pdb=" O GLY B4542 " (cutoff:3.500A) Processing helix chain 'B' and resid 4558 through 4578 Processing helix chain 'B' and resid 4638 through 4665 removed outlier: 3.572A pdb=" N LEU B4652 " --> pdb=" O LEU B4648 " (cutoff:3.500A) Processing helix chain 'B' and resid 4665 through 4683 removed outlier: 3.504A pdb=" N VAL B4669 " --> pdb=" O LYS B4665 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4703 Processing helix chain 'B' and resid 4704 through 4706 No H-bonds generated for 'chain 'B' and resid 4704 through 4706' Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 5.068A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4734 through 4742 Processing helix chain 'B' and resid 4773 through 4786 removed outlier: 3.501A pdb=" N ASP B4786 " --> pdb=" O VAL B4782 " (cutoff:3.500A) Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.974A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4813 Processing helix chain 'B' and resid 4814 through 4820 removed outlier: 4.012A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.769A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.348A 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 4878 through 4893 removed outlier: 4.334A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4925 removed outlier: 3.587A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) Processing helix chain 'B' and resid 4926 through 4957 removed outlier: 4.586A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B4933 " --> pdb=" O LEU B4929 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 3.934A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 4999 through 5003 Processing helix chain 'B' and resid 5004 through 5016 Processing helix chain 'B' and resid 5027 through 5032 Processing helix chain 'B' and resid 5032 through 5037 Processing helix chain 'C' and resid 3951 through 3970 Processing helix chain 'C' and resid 3973 through 3982 Processing helix chain 'C' and resid 3984 through 3990 Processing helix chain 'C' and resid 3992 through 4006 removed outlier: 4.012A pdb=" N MET C4000 " --> pdb=" O PHE C3996 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4031 Processing helix chain 'C' and resid 4038 through 4051 removed outlier: 3.509A pdb=" N VAL C4045 " --> pdb=" O ALA C4041 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP C4046 " --> pdb=" O ARG C4042 " (cutoff:3.500A) Processing helix chain 'C' and resid 4051 through 4060 Processing helix chain 'C' and resid 4198 through 4206 Processing helix chain 'C' and resid 4207 through 4224 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4541 through 4558 removed outlier: 3.771A pdb=" N VAL C4546 " --> pdb=" O GLY C4542 " (cutoff:3.500A) Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4665 removed outlier: 3.571A pdb=" N LEU C4652 " --> pdb=" O LEU C4648 " (cutoff:3.500A) Processing helix chain 'C' and resid 4665 through 4683 removed outlier: 3.504A pdb=" N VAL C4669 " --> pdb=" O LYS C4665 " (cutoff:3.500A) Processing helix chain 'C' and resid 4696 through 4703 Processing helix chain 'C' and resid 4704 through 4706 No H-bonds generated for 'chain 'C' and resid 4704 through 4706' Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 5.068A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4734 through 4742 Processing helix chain 'C' and resid 4773 through 4786 removed outlier: 3.501A pdb=" N ASP C4786 " --> pdb=" O VAL C4782 " (cutoff:3.500A) Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.971A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4813 Processing helix chain 'C' and resid 4814 through 4820 removed outlier: 4.012A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.768A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.349A 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 4878 through 4893 removed outlier: 4.334A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4925 removed outlier: 3.587A pdb=" N VAL C4915 " --> pdb=" O LEU C4911 " (cutoff:3.500A) Processing helix chain 'C' and resid 4926 through 4957 removed outlier: 4.586A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C4933 " --> pdb=" O LEU C4929 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 3.935A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 4999 through 5003 Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5032 Processing helix chain 'C' and resid 5032 through 5037 Processing helix chain 'D' and resid 3951 through 3970 Processing helix chain 'D' and resid 3973 through 3982 Processing helix chain 'D' and resid 3984 through 3990 Processing helix chain 'D' and resid 3992 through 4006 removed outlier: 4.012A pdb=" N MET D4000 " --> pdb=" O PHE D3996 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4031 Processing helix chain 'D' and resid 4038 through 4051 removed outlier: 3.509A pdb=" N VAL D4045 " --> pdb=" O ALA D4041 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D4046 " --> pdb=" O ARG D4042 " (cutoff:3.500A) Processing helix chain 'D' and resid 4051 through 4060 Processing helix chain 'D' and resid 4198 through 4206 Processing helix chain 'D' and resid 4207 through 4224 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4541 through 4558 removed outlier: 3.771A pdb=" N VAL D4546 " --> pdb=" O GLY D4542 " (cutoff:3.500A) Processing helix chain 'D' and resid 4558 through 4578 Processing helix chain 'D' and resid 4638 through 4665 removed outlier: 3.572A pdb=" N LEU D4652 " --> pdb=" O LEU D4648 " (cutoff:3.500A) Processing helix chain 'D' and resid 4665 through 4683 removed outlier: 3.504A pdb=" N VAL D4669 " --> pdb=" O LYS D4665 " (cutoff:3.500A) Processing helix chain 'D' and resid 4696 through 4703 Processing helix chain 'D' and resid 4704 through 4706 No H-bonds generated for 'chain 'D' and resid 4704 through 4706' Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 5.068A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4734 through 4742 Processing helix chain 'D' and resid 4773 through 4786 removed outlier: 3.501A pdb=" N ASP D4786 " --> pdb=" O VAL D4782 " (cutoff:3.500A) Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.974A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4813 Processing helix chain 'D' and resid 4814 through 4820 removed outlier: 4.012A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.768A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.348A 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 4878 through 4893 removed outlier: 4.334A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4925 removed outlier: 3.587A pdb=" N VAL D4915 " --> pdb=" O LEU D4911 " (cutoff:3.500A) Processing helix chain 'D' and resid 4926 through 4957 removed outlier: 4.586A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D4933 " --> pdb=" O LEU D4929 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 3.935A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 4999 through 5003 Processing helix chain 'D' and resid 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5032 Processing helix chain 'D' and resid 5032 through 5037 Processing sheet with id=AA1, first strand: chain 'A' and resid 4178 through 4184 Processing sheet with id=AA2, first strand: chain 'A' and resid 4580 through 4583 removed outlier: 3.784A pdb=" N PHE A4631 " --> pdb=" O LYS A4581 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A4583 " --> pdb=" O TYR A4629 " (cutoff:3.500A) 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 removed outlier: 3.784A pdb=" N PHE B4631 " --> pdb=" O LYS B4581 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B4583 " --> pdb=" O TYR B4629 " (cutoff:3.500A) 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 removed outlier: 3.784A pdb=" N PHE C4631 " --> pdb=" O LYS C4581 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C4583 " --> pdb=" O TYR C4629 " (cutoff:3.500A) 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 removed outlier: 3.784A pdb=" N PHE D4631 " --> pdb=" O LYS D4581 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D4583 " --> pdb=" O TYR D4629 " (cutoff:3.500A) 1354 hydrogen bonds defined for protein. 3966 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: 6.42 Time building geometry restraints manager: 6.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 6715 1.37 - 1.52: 7056 1.52 - 1.66: 7073 1.66 - 1.80: 236 1.80 - 1.95: 44 Bond restraints: 21124 Sorted by residual: bond pdb=" CA LEU C4578 " pdb=" C LEU C4578 " ideal model delta sigma weight residual 1.523 1.545 -0.021 1.34e-02 5.57e+03 2.54e+00 bond pdb=" CA LEU B4578 " pdb=" C LEU B4578 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.34e-02 5.57e+03 2.34e+00 bond pdb=" CA LEU D4578 " pdb=" C LEU D4578 " ideal model delta sigma weight residual 1.523 1.543 -0.020 1.34e-02 5.57e+03 2.28e+00 bond pdb=" CA LEU A4578 " pdb=" C LEU A4578 " ideal model delta sigma weight residual 1.523 1.543 -0.020 1.34e-02 5.57e+03 2.28e+00 bond pdb=" N VAL C3990 " pdb=" CA VAL C3990 " ideal model delta sigma weight residual 1.474 1.456 0.019 1.57e-02 4.06e+03 1.41e+00 ... (remaining 21119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 27840 1.47 - 2.93: 538 2.93 - 4.40: 134 4.40 - 5.87: 16 5.87 - 7.33: 8 Bond angle restraints: 28536 Sorted by residual: angle pdb=" CB LYS C4060 " pdb=" CG LYS C4060 " pdb=" CD LYS C4060 " ideal model delta sigma weight residual 111.30 118.63 -7.33 2.30e+00 1.89e-01 1.02e+01 angle pdb=" CB LYS A4060 " pdb=" CG LYS A4060 " pdb=" CD LYS A4060 " ideal model delta sigma weight residual 111.30 118.59 -7.29 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CB LYS B4060 " pdb=" CG LYS B4060 " pdb=" CD LYS B4060 " ideal model delta sigma weight residual 111.30 118.59 -7.29 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CB LYS D4060 " pdb=" CG LYS D4060 " pdb=" CD LYS D4060 " ideal model delta sigma weight residual 111.30 118.58 -7.28 2.30e+00 1.89e-01 1.00e+01 angle pdb=" C VAL C3989 " pdb=" N VAL C3990 " pdb=" CA VAL C3990 " ideal model delta sigma weight residual 121.65 118.96 2.69 9.40e-01 1.13e+00 8.19e+00 ... (remaining 28531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.52: 11984 29.52 - 59.05: 392 59.05 - 88.57: 48 88.57 - 118.09: 4 118.09 - 147.62: 4 Dihedral angle restraints: 12432 sinusoidal: 5120 harmonic: 7312 Sorted by residual: dihedral pdb=" CA GLY C3971 " pdb=" C GLY C3971 " pdb=" N PRO C3972 " pdb=" CA PRO C3972 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLY D3971 " pdb=" C GLY D3971 " pdb=" N PRO D3972 " pdb=" CA PRO D3972 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLY B3971 " pdb=" C GLY B3971 " pdb=" N PRO B3972 " pdb=" CA PRO B3972 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 12429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2147 0.034 - 0.068: 739 0.068 - 0.102: 146 0.102 - 0.136: 48 0.136 - 0.170: 4 Chirality restraints: 3084 Sorted by residual: chirality pdb=" CA GLU B4640 " pdb=" N GLU B4640 " pdb=" C GLU B4640 " pdb=" CB GLU B4640 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA GLU A4640 " pdb=" N GLU A4640 " pdb=" C GLU A4640 " pdb=" CB GLU A4640 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA GLU D4640 " pdb=" N GLU D4640 " pdb=" C GLU D4640 " pdb=" CB GLU D4640 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 3081 not shown) Planarity restraints: 3596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D4244 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" CD GLU D4244 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU D4244 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D4244 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C4244 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" CD GLU C4244 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU C4244 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C4244 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A4244 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" CD GLU A4244 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU A4244 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A4244 " -0.009 2.00e-02 2.50e+03 ... (remaining 3593 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3885 2.77 - 3.30: 20412 3.30 - 3.83: 34371 3.83 - 4.37: 39424 4.37 - 4.90: 68157 Nonbonded interactions: 166249 Sorted by model distance: nonbonded pdb=" NE1 TRP C3986 " pdb=" OE1 GLN C4043 " model vdw 2.236 3.120 nonbonded pdb=" NE1 TRP D3986 " pdb=" OE1 GLN D4043 " model vdw 2.237 3.120 nonbonded pdb=" OH TYR C4661 " pdb=" OD2 ASP C4786 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A4661 " pdb=" OD2 ASP A4786 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR D4661 " pdb=" OD2 ASP D4786 " model vdw 2.287 3.040 ... (remaining 166244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 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: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 50.230 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.003 0.041 21124 Z= 0.174 Angle : 0.532 7.335 28536 Z= 0.301 Chirality : 0.037 0.170 3084 Planarity : 0.003 0.035 3596 Dihedral : 14.621 147.616 7708 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), residues: 2464 helix: 1.82 (0.12), residues: 1680 sheet: -0.07 (0.76), residues: 64 loop : -0.19 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3986 HIS 0.002 0.001 HIS C4803 PHE 0.022 0.001 PHE C4571 TYR 0.012 0.001 TYR C4580 ARG 0.003 0.000 ARG B4892 *********************** 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 412 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 2.426 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.3134 time to fit residues: 200.7433 Evaluate side-chains 361 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 126 optimal weight: 0.0050 chunk 100 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 0.0770 chunk 144 optimal weight: 0.6980 chunk 225 optimal weight: 0.9980 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN B4020 GLN C3994 HIS C4020 GLN D3994 HIS D4020 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21124 Z= 0.154 Angle : 0.513 7.148 28536 Z= 0.278 Chirality : 0.038 0.139 3084 Planarity : 0.003 0.034 3596 Dihedral : 9.354 149.282 2776 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2464 helix: 1.87 (0.12), residues: 1752 sheet: 0.69 (0.57), residues: 104 loop : 0.10 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C3986 HIS 0.007 0.001 HIS C3994 PHE 0.010 0.001 PHE A4631 TYR 0.011 0.001 TYR D3968 ARG 0.004 0.000 ARG D4892 *********************** 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 375 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 2.483 Fit side-chains REVERT: A 3994 HIS cc_start: 0.7502 (t70) cc_final: 0.6987 (t-90) REVERT: A 3998 HIS cc_start: 0.8131 (m90) cc_final: 0.7231 (m90) REVERT: A 4029 SER cc_start: 0.8970 (t) cc_final: 0.8633 (p) REVERT: B 3994 HIS cc_start: 0.7497 (t70) cc_final: 0.6975 (t-90) REVERT: B 3998 HIS cc_start: 0.8131 (m90) cc_final: 0.7227 (m90) REVERT: B 4029 SER cc_start: 0.8968 (t) cc_final: 0.8624 (p) REVERT: C 4029 SER cc_start: 0.8943 (t) cc_final: 0.8654 (p) REVERT: D 4029 SER cc_start: 0.8946 (t) cc_final: 0.8657 (p) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.3075 time to fit residues: 181.4296 Evaluate side-chains 359 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 0.3980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C3994 HIS D3994 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21124 Z= 0.207 Angle : 0.498 7.292 28536 Z= 0.270 Chirality : 0.038 0.134 3084 Planarity : 0.003 0.032 3596 Dihedral : 9.382 149.218 2776 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.18 % Allowed : 9.14 % Favored : 90.68 % 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: 1.76 (0.17), residues: 2464 helix: 1.78 (0.12), residues: 1772 sheet: 0.73 (0.56), residues: 104 loop : -0.61 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C3986 HIS 0.006 0.001 HIS D3994 PHE 0.012 0.001 PHE C4921 TYR 0.012 0.001 TYR A4580 ARG 0.005 0.000 ARG D4892 *********************** 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 362 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 358 time to evaluate : 2.451 Fit side-chains REVERT: A 3957 VAL cc_start: 0.8379 (t) cc_final: 0.8127 (p) REVERT: A 4029 SER cc_start: 0.8911 (t) cc_final: 0.8643 (p) REVERT: B 3957 VAL cc_start: 0.8351 (t) cc_final: 0.8102 (p) REVERT: B 4029 SER cc_start: 0.8914 (t) cc_final: 0.8634 (p) REVERT: C 3957 VAL cc_start: 0.8353 (t) cc_final: 0.8098 (p) REVERT: C 3992 PHE cc_start: 0.8413 (m-80) cc_final: 0.8141 (m-80) REVERT: D 3957 VAL cc_start: 0.8372 (t) cc_final: 0.8112 (p) REVERT: D 3992 PHE cc_start: 0.8414 (m-80) cc_final: 0.8142 (m-80) outliers start: 4 outliers final: 2 residues processed: 360 average time/residue: 0.3096 time to fit residues: 175.0275 Evaluate side-chains 334 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 332 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain D residue 3989 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 226 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 chunk 118 optimal weight: 0.0570 chunk 214 optimal weight: 0.0670 chunk 64 optimal weight: 0.0000 overall best weight: 0.3840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4626 ASN C3994 HIS C4626 ASN D3994 HIS D4626 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21124 Z= 0.125 Angle : 0.454 7.135 28536 Z= 0.248 Chirality : 0.036 0.134 3084 Planarity : 0.003 0.033 3596 Dihedral : 9.272 151.114 2776 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.67 % Allowed : 10.53 % Favored : 88.80 % 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: 2.02 (0.17), residues: 2464 helix: 2.00 (0.12), residues: 1772 sheet: 0.90 (0.57), residues: 104 loop : -0.64 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B4644 HIS 0.003 0.000 HIS C3994 PHE 0.006 0.001 PHE B4916 TYR 0.008 0.001 TYR D4580 ARG 0.005 0.000 ARG B4892 *********************** 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 370 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 355 time to evaluate : 2.405 Fit side-chains REVERT: A 3957 VAL cc_start: 0.8441 (t) cc_final: 0.8172 (p) REVERT: A 3992 PHE cc_start: 0.8481 (m-80) cc_final: 0.8208 (m-80) REVERT: A 4851 TYR cc_start: 0.7413 (m-80) cc_final: 0.7018 (m-80) REVERT: B 3957 VAL cc_start: 0.8416 (t) cc_final: 0.8151 (p) REVERT: B 3992 PHE cc_start: 0.8482 (m-80) cc_final: 0.8208 (m-80) REVERT: B 4851 TYR cc_start: 0.7412 (m-80) cc_final: 0.7013 (m-80) REVERT: C 3957 VAL cc_start: 0.8340 (t) cc_final: 0.8051 (p) REVERT: C 3992 PHE cc_start: 0.8370 (m-80) cc_final: 0.8153 (m-80) REVERT: C 4851 TYR cc_start: 0.7415 (m-80) cc_final: 0.7019 (m-80) REVERT: D 3957 VAL cc_start: 0.8358 (t) cc_final: 0.8065 (p) REVERT: D 3992 PHE cc_start: 0.8369 (m-80) cc_final: 0.8157 (m-80) REVERT: D 4851 TYR cc_start: 0.7415 (m-80) cc_final: 0.7022 (m-80) outliers start: 15 outliers final: 7 residues processed: 368 average time/residue: 0.3000 time to fit residues: 175.4706 Evaluate side-chains 348 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 341 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4039 MET Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 4039 MET Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 165 optimal weight: 0.0020 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C3994 HIS D3994 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21124 Z= 0.196 Angle : 0.495 7.197 28536 Z= 0.266 Chirality : 0.037 0.132 3084 Planarity : 0.003 0.034 3596 Dihedral : 9.188 149.562 2776 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.40 % Allowed : 12.37 % Favored : 87.23 % 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: 1.87 (0.17), residues: 2464 helix: 1.87 (0.12), residues: 1772 sheet: 1.00 (0.58), residues: 104 loop : -0.62 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A3986 HIS 0.004 0.001 HIS D3994 PHE 0.011 0.001 PHE D4921 TYR 0.012 0.001 TYR C4580 ARG 0.005 0.000 ARG C4892 *********************** 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 355 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 346 time to evaluate : 2.628 Fit side-chains REVERT: A 3992 PHE cc_start: 0.8484 (m-80) cc_final: 0.8257 (m-80) REVERT: A 4043 GLN cc_start: 0.7393 (tt0) cc_final: 0.7180 (tt0) REVERT: A 4743 MET cc_start: 0.7160 (ptm) cc_final: 0.6777 (ptt) REVERT: B 3992 PHE cc_start: 0.8484 (m-80) cc_final: 0.8257 (m-80) REVERT: B 4043 GLN cc_start: 0.7409 (tt0) cc_final: 0.7188 (tt0) REVERT: B 4743 MET cc_start: 0.7161 (ptm) cc_final: 0.6776 (ptt) REVERT: C 3957 VAL cc_start: 0.8312 (t) cc_final: 0.8064 (p) REVERT: C 4047 MET cc_start: 0.7533 (ttp) cc_final: 0.7280 (ttm) REVERT: C 4743 MET cc_start: 0.7152 (ptm) cc_final: 0.6768 (ptt) REVERT: D 3957 VAL cc_start: 0.8329 (t) cc_final: 0.8080 (p) REVERT: D 4047 MET cc_start: 0.7521 (ttp) cc_final: 0.7267 (ttm) REVERT: D 4743 MET cc_start: 0.7151 (ptm) cc_final: 0.6769 (ptt) outliers start: 9 outliers final: 4 residues processed: 355 average time/residue: 0.3193 time to fit residues: 177.1108 Evaluate side-chains 326 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 322 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 140 optimal weight: 0.2980 chunk 59 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4886 HIS B4886 HIS C3994 HIS C4886 HIS D3994 HIS D4886 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21124 Z= 0.214 Angle : 0.492 7.287 28536 Z= 0.265 Chirality : 0.037 0.133 3084 Planarity : 0.003 0.034 3596 Dihedral : 9.129 150.039 2776 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.54 % Allowed : 12.86 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.17), residues: 2464 helix: 1.89 (0.12), residues: 1768 sheet: 0.94 (0.58), residues: 104 loop : -0.68 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B3986 HIS 0.004 0.001 HIS D4803 PHE 0.011 0.001 PHE D4921 TYR 0.013 0.001 TYR B4580 ARG 0.005 0.000 ARG B4892 *********************** 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 348 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 336 time to evaluate : 2.446 Fit side-chains REVERT: A 4743 MET cc_start: 0.7076 (ptm) cc_final: 0.6636 (ptt) REVERT: A 4796 MET cc_start: 0.7856 (tpt) cc_final: 0.7553 (tpt) REVERT: A 4851 TYR cc_start: 0.7474 (m-80) cc_final: 0.7020 (m-80) REVERT: B 4043 GLN cc_start: 0.7444 (tt0) cc_final: 0.7239 (tt0) REVERT: B 4743 MET cc_start: 0.7076 (ptm) cc_final: 0.6636 (ptt) REVERT: B 4796 MET cc_start: 0.7854 (tpt) cc_final: 0.7559 (tpt) REVERT: B 4851 TYR cc_start: 0.7469 (m-80) cc_final: 0.6994 (m-80) REVERT: C 4047 MET cc_start: 0.7346 (ttp) cc_final: 0.7067 (ttt) REVERT: C 4212 GLU cc_start: 0.7152 (tp30) cc_final: 0.6865 (tp30) REVERT: C 4743 MET cc_start: 0.7066 (ptm) cc_final: 0.6629 (ptt) REVERT: C 4796 MET cc_start: 0.7857 (tpt) cc_final: 0.7557 (tpt) REVERT: C 4851 TYR cc_start: 0.7476 (m-80) cc_final: 0.7017 (m-80) REVERT: D 4047 MET cc_start: 0.7348 (ttp) cc_final: 0.7076 (ttt) REVERT: D 4212 GLU cc_start: 0.7150 (tp30) cc_final: 0.6861 (tp30) REVERT: D 4743 MET cc_start: 0.7063 (ptm) cc_final: 0.6628 (ptt) REVERT: D 4796 MET cc_start: 0.7856 (tpt) cc_final: 0.7553 (tpt) REVERT: D 4851 TYR cc_start: 0.7478 (m-80) cc_final: 0.7022 (m-80) outliers start: 12 outliers final: 8 residues processed: 348 average time/residue: 0.3030 time to fit residues: 166.6632 Evaluate side-chains 331 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 323 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 3974 THR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 3974 THR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 3974 THR Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 149 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C3994 HIS D3994 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21124 Z= 0.155 Angle : 0.472 7.675 28536 Z= 0.256 Chirality : 0.036 0.132 3084 Planarity : 0.003 0.035 3596 Dihedral : 9.002 150.506 2776 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.54 % Allowed : 12.32 % Favored : 87.14 % 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: 1.97 (0.17), residues: 2464 helix: 1.97 (0.12), residues: 1768 sheet: 0.93 (0.57), residues: 104 loop : -0.65 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D3986 HIS 0.004 0.001 HIS D3994 PHE 0.008 0.001 PHE D3962 TYR 0.010 0.001 TYR C4580 ARG 0.005 0.000 ARG D4892 *********************** REFINEMENT MACRO_CYCLE 7 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 345 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 333 time to evaluate : 2.644 Fit side-chains REVERT: A 4743 MET cc_start: 0.7195 (ptm) cc_final: 0.6782 (ptt) REVERT: A 4851 TYR cc_start: 0.7458 (m-80) cc_final: 0.7031 (m-80) REVERT: B 3986 TRP cc_start: 0.8303 (m100) cc_final: 0.7958 (m100) REVERT: B 4047 MET cc_start: 0.6415 (ttt) cc_final: 0.6176 (ttm) REVERT: B 4743 MET cc_start: 0.7194 (ptm) cc_final: 0.6783 (ptt) REVERT: B 4851 TYR cc_start: 0.7455 (m-80) cc_final: 0.7027 (m-80) REVERT: C 4043 GLN cc_start: 0.7887 (mt0) cc_final: 0.7522 (mt0) REVERT: C 4212 GLU cc_start: 0.7176 (tp30) cc_final: 0.6917 (tp30) REVERT: C 4743 MET cc_start: 0.7185 (ptm) cc_final: 0.6774 (ptt) REVERT: C 4851 TYR cc_start: 0.7458 (m-80) cc_final: 0.7032 (m-80) REVERT: D 4043 GLN cc_start: 0.7914 (mt0) cc_final: 0.7532 (mt0) REVERT: D 4212 GLU cc_start: 0.7174 (tp30) cc_final: 0.6918 (tp30) REVERT: D 4743 MET cc_start: 0.7183 (ptm) cc_final: 0.6773 (ptt) REVERT: D 4851 TYR cc_start: 0.7462 (m-80) cc_final: 0.7033 (m-80) outliers start: 12 outliers final: 8 residues processed: 341 average time/residue: 0.3151 time to fit residues: 168.9174 Evaluate side-chains 326 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 318 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 3974 THR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 4022 ASP Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 4022 ASP Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.4980 chunk 95 optimal weight: 0.0980 chunk 142 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4558 ASN B4558 ASN C3994 HIS C4558 ASN D3994 HIS D4558 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21124 Z= 0.142 Angle : 0.467 7.639 28536 Z= 0.253 Chirality : 0.036 0.133 3084 Planarity : 0.003 0.034 3596 Dihedral : 8.870 150.211 2776 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.27 % Allowed : 12.63 % Favored : 87.10 % 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: 2.04 (0.17), residues: 2464 helix: 1.95 (0.12), residues: 1792 sheet: 0.97 (0.57), residues: 104 loop : -0.45 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D3986 HIS 0.004 0.000 HIS D3994 PHE 0.009 0.001 PHE D3962 TYR 0.014 0.001 TYR C4554 ARG 0.005 0.000 ARG A4892 *********************** REFINEMENT MACRO_CYCLE 8 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 333 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 327 time to evaluate : 2.382 Fit side-chains REVERT: A 4212 GLU cc_start: 0.7158 (tp30) cc_final: 0.6904 (tp30) REVERT: A 4743 MET cc_start: 0.7077 (ptm) cc_final: 0.6619 (ptt) REVERT: A 4796 MET cc_start: 0.7889 (tpt) cc_final: 0.7632 (tpt) REVERT: A 4851 TYR cc_start: 0.7474 (m-80) cc_final: 0.7094 (m-80) REVERT: B 3986 TRP cc_start: 0.8304 (m100) cc_final: 0.8043 (m100) REVERT: B 4047 MET cc_start: 0.6365 (ttt) cc_final: 0.6162 (ttm) REVERT: B 4212 GLU cc_start: 0.7155 (tp30) cc_final: 0.6907 (tp30) REVERT: B 4743 MET cc_start: 0.7073 (ptm) cc_final: 0.6618 (ptt) REVERT: B 4796 MET cc_start: 0.7888 (tpt) cc_final: 0.7641 (tpt) REVERT: B 4851 TYR cc_start: 0.7473 (m-80) cc_final: 0.7091 (m-80) REVERT: C 4212 GLU cc_start: 0.7163 (tp30) cc_final: 0.6906 (tp30) REVERT: C 4743 MET cc_start: 0.7063 (ptm) cc_final: 0.6606 (ptt) REVERT: C 4796 MET cc_start: 0.7888 (tpt) cc_final: 0.7637 (tpt) REVERT: C 4851 TYR cc_start: 0.7476 (m-80) cc_final: 0.7095 (m-80) REVERT: D 4212 GLU cc_start: 0.7155 (tp30) cc_final: 0.6902 (tp30) REVERT: D 4743 MET cc_start: 0.7060 (ptm) cc_final: 0.6607 (ptt) REVERT: D 4796 MET cc_start: 0.7887 (tpt) cc_final: 0.7630 (tpt) REVERT: D 4851 TYR cc_start: 0.7478 (m-80) cc_final: 0.7095 (m-80) outliers start: 6 outliers final: 6 residues processed: 331 average time/residue: 0.3240 time to fit residues: 170.1047 Evaluate side-chains 326 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 320 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 4022 ASP Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 4022 ASP Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 97 optimal weight: 0.0570 chunk 174 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 0.2980 chunk 146 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS B3994 HIS C3994 HIS D3994 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21124 Z= 0.138 Angle : 0.467 7.746 28536 Z= 0.253 Chirality : 0.036 0.133 3084 Planarity : 0.003 0.034 3596 Dihedral : 8.685 149.800 2776 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.45 % Allowed : 12.50 % Favored : 87.05 % 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: 2.09 (0.17), residues: 2464 helix: 1.99 (0.12), residues: 1792 sheet: 0.95 (0.57), residues: 104 loop : -0.47 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D3986 HIS 0.005 0.001 HIS A3994 PHE 0.011 0.001 PHE A3962 TYR 0.014 0.001 TYR A4554 ARG 0.005 0.000 ARG A4892 *********************** REFINEMENT MACRO_CYCLE 9 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 332 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 322 time to evaluate : 2.488 Fit side-chains REVERT: A 4212 GLU cc_start: 0.7149 (tp30) cc_final: 0.6900 (tp30) REVERT: A 4732 PHE cc_start: 0.7884 (t80) cc_final: 0.7499 (t80) REVERT: A 4743 MET cc_start: 0.7084 (ptm) cc_final: 0.6617 (ptt) REVERT: A 4796 MET cc_start: 0.7875 (tpt) cc_final: 0.7606 (tpt) REVERT: A 4851 TYR cc_start: 0.7472 (m-80) cc_final: 0.7082 (m-80) REVERT: B 4212 GLU cc_start: 0.7145 (tp30) cc_final: 0.6902 (tp30) REVERT: B 4732 PHE cc_start: 0.7884 (t80) cc_final: 0.7497 (t80) REVERT: B 4743 MET cc_start: 0.7082 (ptm) cc_final: 0.6618 (ptt) REVERT: B 4796 MET cc_start: 0.7872 (tpt) cc_final: 0.7610 (tpt) REVERT: B 4851 TYR cc_start: 0.7470 (m-80) cc_final: 0.7079 (m-80) REVERT: C 4212 GLU cc_start: 0.7151 (tp30) cc_final: 0.6902 (tp30) REVERT: C 4732 PHE cc_start: 0.7886 (t80) cc_final: 0.7496 (t80) REVERT: C 4743 MET cc_start: 0.7071 (ptm) cc_final: 0.6606 (ptt) REVERT: C 4796 MET cc_start: 0.7871 (tpt) cc_final: 0.7610 (tpt) REVERT: C 4851 TYR cc_start: 0.7470 (m-80) cc_final: 0.7080 (m-80) REVERT: D 4212 GLU cc_start: 0.7147 (tp30) cc_final: 0.6901 (tp30) REVERT: D 4732 PHE cc_start: 0.7884 (t80) cc_final: 0.7498 (t80) REVERT: D 4743 MET cc_start: 0.7069 (ptm) cc_final: 0.6605 (ptt) REVERT: D 4796 MET cc_start: 0.7875 (tpt) cc_final: 0.7606 (tpt) REVERT: D 4851 TYR cc_start: 0.7473 (m-80) cc_final: 0.7082 (m-80) outliers start: 10 outliers final: 8 residues processed: 328 average time/residue: 0.3137 time to fit residues: 161.0428 Evaluate side-chains 328 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 320 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 3974 THR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 4022 ASP Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 4022 ASP Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 247 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS ** A4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS C3994 HIS D3994 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21124 Z= 0.189 Angle : 0.495 8.003 28536 Z= 0.266 Chirality : 0.037 0.134 3084 Planarity : 0.003 0.034 3596 Dihedral : 8.579 148.644 2776 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.36 % Allowed : 12.72 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.17), residues: 2464 helix: 2.00 (0.12), residues: 1772 sheet: 0.93 (0.57), residues: 104 loop : -0.63 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C3986 HIS 0.005 0.001 HIS B3994 PHE 0.010 0.001 PHE C4921 TYR 0.013 0.001 TYR A4554 ARG 0.005 0.000 ARG A4892 ********************** REFINEMENT MACRO_CYCLE 10 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 331 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 323 time to evaluate : 2.632 Fit side-chains REVERT: A 3986 TRP cc_start: 0.7825 (m100) cc_final: 0.7302 (m100) REVERT: A 4743 MET cc_start: 0.7099 (ptm) cc_final: 0.6645 (ptt) REVERT: A 4796 MET cc_start: 0.7873 (tpt) cc_final: 0.7593 (tpt) REVERT: A 4851 TYR cc_start: 0.7625 (m-80) cc_final: 0.7220 (m-80) REVERT: B 4212 GLU cc_start: 0.7131 (tp30) cc_final: 0.6854 (tp30) REVERT: B 4743 MET cc_start: 0.7098 (ptm) cc_final: 0.6646 (ptt) REVERT: B 4796 MET cc_start: 0.7872 (tpt) cc_final: 0.7605 (tpt) REVERT: B 4851 TYR cc_start: 0.7625 (m-80) cc_final: 0.7214 (m-80) REVERT: C 3992 PHE cc_start: 0.8419 (m-80) cc_final: 0.8135 (m-80) REVERT: C 4212 GLU cc_start: 0.7139 (tp30) cc_final: 0.6849 (tp30) REVERT: C 4743 MET cc_start: 0.7090 (ptm) cc_final: 0.6636 (ptt) REVERT: C 4796 MET cc_start: 0.7872 (tpt) cc_final: 0.7600 (tpt) REVERT: C 4851 TYR cc_start: 0.7626 (m-80) cc_final: 0.7216 (m-80) REVERT: D 3992 PHE cc_start: 0.8421 (m-80) cc_final: 0.8138 (m-80) REVERT: D 4212 GLU cc_start: 0.7138 (tp30) cc_final: 0.6853 (tp30) REVERT: D 4743 MET cc_start: 0.7085 (ptm) cc_final: 0.6633 (ptt) REVERT: D 4796 MET cc_start: 0.7872 (tpt) cc_final: 0.7595 (tpt) REVERT: D 4851 TYR cc_start: 0.7629 (m-80) cc_final: 0.7222 (m-80) outliers start: 8 outliers final: 7 residues processed: 330 average time/residue: 0.3161 time to fit residues: 163.0292 Evaluate side-chains 327 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 320 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 3974 THR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 3974 THR Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 0.0060 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 173 optimal weight: 0.2980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS ** A4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS C3994 HIS D3994 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124646 restraints weight = 29419.594| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.88 r_work: 0.3338 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21124 Z= 0.137 Angle : 0.472 7.687 28536 Z= 0.254 Chirality : 0.036 0.133 3084 Planarity : 0.003 0.035 3596 Dihedral : 8.403 149.093 2776 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.31 % Allowed : 12.54 % Favored : 87.14 % 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: 2.15 (0.17), residues: 2464 helix: 2.04 (0.12), residues: 1792 sheet: 0.96 (0.56), residues: 104 loop : -0.46 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C3986 HIS 0.004 0.001 HIS B3994 PHE 0.011 0.001 PHE B3962 TYR 0.007 0.001 TYR D4580 ARG 0.005 0.000 ARG B4892 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4707.42 seconds wall clock time: 86 minutes 33.79 seconds (5193.79 seconds total)