Starting phenix.real_space_refine on Wed Aug 7 19:51:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seu_40429/08_2024/8seu_40429.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seu_40429/08_2024/8seu_40429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seu_40429/08_2024/8seu_40429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seu_40429/08_2024/8seu_40429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seu_40429/08_2024/8seu_40429.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seu_40429/08_2024/8seu_40429.cif" } resolution = 3.0 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= -0.002 sd= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 160 5.16 5 C 13384 2.51 5 N 3272 2.21 5 O 3756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4690": "OE1" <-> "OE2" Residue "A ASP 4694": "OD1" <-> "OD2" Residue "A PHE 4959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4690": "OE1" <-> "OE2" Residue "B ASP 4694": "OD1" <-> "OD2" Residue "B PHE 4959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4690": "OE1" <-> "OE2" Residue "C ASP 4694": "OD1" <-> "OD2" Residue "C PHE 4959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4690": "OE1" <-> "OE2" Residue "D ASP 4694": "OD1" <-> "OD2" Residue "D PHE 4959": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20576 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5143 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 4 Chain: "B" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5143 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 4 Chain: "C" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5143 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 4 Chain: "D" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5143 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4469 SG CYS A4958 56.100 81.158 87.429 1.00 52.07 S ATOM 4494 SG CYS A4961 58.240 82.382 90.402 1.00 46.03 S ATOM 9612 SG CYS B4958 60.522 56.100 87.429 1.00 52.07 S ATOM 9637 SG CYS B4961 59.298 58.240 90.402 1.00 46.03 S ATOM 14755 SG CYS C4958 85.580 60.522 87.429 1.00 52.07 S ATOM 14780 SG CYS C4961 83.440 59.298 90.402 1.00 46.03 S ATOM 19898 SG CYS D4958 81.158 85.580 87.429 1.00 52.07 S ATOM 19923 SG CYS D4961 82.382 83.440 90.402 1.00 46.03 S Time building chain proxies: 11.73, per 1000 atoms: 0.57 Number of scatterers: 20576 At special positions: 0 Unit cell: (142.968, 142.968, 135.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 160 16.00 O 3756 8.00 N 3272 7.00 C 13384 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 - 3.50 Amino acid : False - 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: 7.61 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5101 " pdb="ZN ZN A5101 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5101 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5101 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5101 " - pdb=" SG CYS A4958 " pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4958 " pdb=" ZN C5101 " pdb="ZN ZN C5101 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5101 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5101 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5101 " - pdb=" SG CYS C4958 " pdb=" ZN D5101 " pdb="ZN ZN D5101 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4958 " Number of angles added : 8 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 79.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 3950 through 3970 Processing helix chain 'A' and resid 3973 through 3982 Processing helix chain 'A' and resid 3984 through 4006 removed outlier: 3.604A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4031 removed outlier: 3.594A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4051 removed outlier: 3.541A pdb=" N MET A4047 " --> pdb=" O GLN A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4060 Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4207 through 4225 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4541 through 4558 Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4665 removed outlier: 3.863A pdb=" N TRP A4644 " --> pdb=" O GLU A4640 " (cutoff:3.500A) Processing helix chain 'A' and resid 4665 through 4685 removed outlier: 3.577A 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: 5.059A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.603A 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 4773 through 4786 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.880A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4814 removed outlier: 3.618A pdb=" N ALA A4810 " --> pdb=" O PHE A4807 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A4811 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A4812 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A4814 " --> pdb=" O ALA A4811 " (cutoff:3.500A) Processing helix chain 'A' and resid 4815 through 4820 Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.619A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.383A 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 Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 4.651A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 4.178A pdb=" N GLU A4900 " --> 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 removed outlier: 3.688A pdb=" N ILE A4936 " --> pdb=" O ILE A4932 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.899A 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 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 Processing helix chain 'B' and resid 3973 through 3982 Processing helix chain 'B' and resid 3984 through 4006 removed outlier: 3.604A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4031 removed outlier: 3.594A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4051 removed outlier: 3.541A pdb=" N MET B4047 " --> pdb=" O GLN B4043 " (cutoff:3.500A) Processing helix chain 'B' and resid 4051 through 4060 Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4207 through 4225 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4541 through 4558 Processing helix chain 'B' and resid 4558 through 4578 Processing helix chain 'B' and resid 4638 through 4665 removed outlier: 3.863A pdb=" N TRP B4644 " --> pdb=" O GLU B4640 " (cutoff:3.500A) Processing helix chain 'B' and resid 4665 through 4685 removed outlier: 3.577A 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: 5.059A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.603A 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 4773 through 4786 Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.880A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4814 removed outlier: 3.618A pdb=" N ALA B4810 " --> pdb=" O PHE B4807 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B4811 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS B4812 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B4814 " --> pdb=" O ALA B4811 " (cutoff:3.500A) Processing helix chain 'B' and resid 4815 through 4820 Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.619A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.383A 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 Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.651A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4901 removed outlier: 4.178A pdb=" N GLU B4900 " --> 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 removed outlier: 3.688A pdb=" N ILE B4936 " --> pdb=" O ILE B4932 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 3.899A 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 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 4006 removed outlier: 3.604A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4031 removed outlier: 3.594A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4051 removed outlier: 3.541A pdb=" N MET C4047 " --> pdb=" O GLN C4043 " (cutoff:3.500A) Processing helix chain 'C' and resid 4051 through 4060 Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4207 through 4225 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4541 through 4558 Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4665 removed outlier: 3.863A pdb=" N TRP C4644 " --> pdb=" O GLU C4640 " (cutoff:3.500A) Processing helix chain 'C' and resid 4665 through 4685 removed outlier: 3.577A 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: 5.059A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.603A 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 4773 through 4786 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.880A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4814 removed outlier: 3.618A pdb=" N ALA C4810 " --> pdb=" O PHE C4807 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C4811 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS C4812 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C4814 " --> pdb=" O ALA C4811 " (cutoff:3.500A) Processing helix chain 'C' and resid 4815 through 4820 Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.619A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.383A 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 Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.651A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 4.178A pdb=" N GLU C4900 " --> 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 removed outlier: 3.688A pdb=" N ILE C4936 " --> pdb=" O ILE C4932 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 3.899A 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 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 4006 removed outlier: 3.604A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4031 removed outlier: 3.594A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4051 removed outlier: 3.541A pdb=" N MET D4047 " --> pdb=" O GLN D4043 " (cutoff:3.500A) Processing helix chain 'D' and resid 4051 through 4060 Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4207 through 4225 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4541 through 4558 Processing helix chain 'D' and resid 4558 through 4578 Processing helix chain 'D' and resid 4638 through 4665 removed outlier: 3.863A pdb=" N TRP D4644 " --> pdb=" O GLU D4640 " (cutoff:3.500A) Processing helix chain 'D' and resid 4665 through 4685 removed outlier: 3.577A 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: 5.059A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.603A 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 4773 through 4786 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.880A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4814 removed outlier: 3.618A pdb=" N ALA D4810 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D4811 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS D4812 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D4814 " --> pdb=" O ALA D4811 " (cutoff:3.500A) Processing helix chain 'D' and resid 4815 through 4820 Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.619A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.383A 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 Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.651A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4901 removed outlier: 4.178A pdb=" N GLU D4900 " --> 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 removed outlier: 3.688A pdb=" N ILE D4936 " --> pdb=" O ILE D4932 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 3.899A 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 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5032 Processing helix chain 'D' and resid 5032 through 5037 Processing sheet with id=AA1, first strand: chain 'A' and resid 4178 through 4184 Processing sheet with id=AA2, first strand: chain 'A' and resid 4580 through 4583 Processing sheet with id=AA3, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id=AA4, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AA5, first strand: chain 'C' and resid 4178 through 4184 Processing sheet with id=AA6, first strand: chain 'C' and resid 4580 through 4583 Processing sheet with id=AA7, first strand: chain 'D' and resid 4178 through 4184 Processing sheet with id=AA8, first strand: chain 'D' and resid 4580 through 4583 1405 hydrogen bonds defined for protein. 4167 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: 6.10 Time building geometry restraints manager: 8.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4452 1.33 - 1.45: 4904 1.45 - 1.57: 11428 1.57 - 1.69: 0 1.69 - 1.81: 276 Bond restraints: 21060 Sorted by residual: bond pdb=" CA SER C3964 " pdb=" CB SER C3964 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.04e+01 bond pdb=" CA SER B3964 " pdb=" CB SER B3964 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.04e+01 bond pdb=" CA SER D3964 " pdb=" CB SER D3964 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.04e+01 bond pdb=" CA SER A3964 " pdb=" CB SER A3964 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.04e+01 bond pdb=" N ASP B4694 " pdb=" CA ASP B4694 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.35e+00 ... (remaining 21055 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.38: 464 106.38 - 113.38: 10928 113.38 - 120.38: 8768 120.38 - 127.38: 8092 127.38 - 134.37: 168 Bond angle restraints: 28420 Sorted by residual: angle pdb=" N ASP A4695 " pdb=" CA ASP A4695 " pdb=" C ASP A4695 " ideal model delta sigma weight residual 113.17 103.98 9.19 1.26e+00 6.30e-01 5.32e+01 angle pdb=" N ASP D4695 " pdb=" CA ASP D4695 " pdb=" C ASP D4695 " ideal model delta sigma weight residual 113.17 103.98 9.19 1.26e+00 6.30e-01 5.32e+01 angle pdb=" N ASP C4695 " pdb=" CA ASP C4695 " pdb=" C ASP C4695 " ideal model delta sigma weight residual 113.17 103.98 9.19 1.26e+00 6.30e-01 5.32e+01 angle pdb=" N ASP B4695 " pdb=" CA ASP B4695 " pdb=" C ASP B4695 " ideal model delta sigma weight residual 113.17 103.98 9.19 1.26e+00 6.30e-01 5.32e+01 angle pdb=" N ASP C4006 " pdb=" CA ASP C4006 " pdb=" C ASP C4006 " ideal model delta sigma weight residual 110.50 119.27 -8.77 1.41e+00 5.03e-01 3.87e+01 ... (remaining 28415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 11524 17.19 - 34.39: 656 34.39 - 51.58: 156 51.58 - 68.77: 44 68.77 - 85.97: 16 Dihedral angle restraints: 12396 sinusoidal: 5060 harmonic: 7336 Sorted by residual: dihedral pdb=" C GLN D4691 " pdb=" N GLN D4691 " pdb=" CA GLN D4691 " pdb=" CB GLN D4691 " ideal model delta harmonic sigma weight residual -122.60 -134.71 12.11 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" C GLN C4691 " pdb=" N GLN C4691 " pdb=" CA GLN C4691 " pdb=" CB GLN C4691 " ideal model delta harmonic sigma weight residual -122.60 -134.71 12.11 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" C GLN A4691 " pdb=" N GLN A4691 " pdb=" CA GLN A4691 " pdb=" CB GLN A4691 " ideal model delta harmonic sigma weight residual -122.60 -134.71 12.11 0 2.50e+00 1.60e-01 2.34e+01 ... (remaining 12393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2744 0.068 - 0.135: 252 0.135 - 0.203: 48 0.203 - 0.270: 20 0.270 - 0.338: 8 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CA GLN C4691 " pdb=" N GLN C4691 " pdb=" C GLN C4691 " pdb=" CB GLN C4691 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA GLN D4691 " pdb=" N GLN D4691 " pdb=" C GLN D4691 " pdb=" CB GLN D4691 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA GLN B4691 " pdb=" N GLN B4691 " pdb=" C GLN B4691 " pdb=" CB GLN B4691 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 3069 not shown) Planarity restraints: 3604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D4693 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C GLY D4693 " 0.036 2.00e-02 2.50e+03 pdb=" O GLY D4693 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP D4694 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C4693 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C GLY C4693 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY C4693 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP C4694 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B4693 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C GLY B4693 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY B4693 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP B4694 " 0.013 2.00e-02 2.50e+03 ... (remaining 3601 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 88 2.48 - 3.08: 14524 3.08 - 3.69: 30795 3.69 - 4.29: 45853 4.29 - 4.90: 76672 Nonbonded interactions: 167932 Sorted by model distance: nonbonded pdb=" OH TYR A4630 " pdb=" NH1 ARG B4860 " model vdw 1.873 3.120 nonbonded pdb=" NH1 ARG A4860 " pdb=" OH TYR D4630 " model vdw 1.873 3.120 nonbonded pdb=" OH TYR B4630 " pdb=" NH1 ARG C4860 " model vdw 1.873 3.120 nonbonded pdb=" OH TYR C4630 " pdb=" NH1 ARG D4860 " model vdw 1.873 3.120 nonbonded pdb=" CD1 LEU C4823 " pdb=" CG MET D4839 " model vdw 2.009 3.860 ... (remaining 167927 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: 5.200 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: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 56.530 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 0.050 21060 Z= 0.296 Angle : 0.718 11.897 28420 Z= 0.486 Chirality : 0.050 0.338 3072 Planarity : 0.004 0.056 3604 Dihedral : 12.630 85.966 7656 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.27 % Favored : 97.41 % Rotamer: Outliers : 1.96 % Allowed : 4.46 % Favored : 93.57 % Cbeta Deviations : 0.34 % 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: 1.51 (0.17), residues: 2472 helix: 1.80 (0.12), residues: 1756 sheet: -0.91 (0.54), residues: 112 loop : -0.97 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B4716 HIS 0.003 0.001 HIS A4803 PHE 0.018 0.001 PHE D4916 TYR 0.013 0.001 TYR A4994 ARG 0.002 0.000 ARG A4563 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 348 time to evaluate : 2.328 Fit side-chains REVERT: A 4245 MET cc_start: 0.8912 (mtt) cc_final: 0.8710 (mtt) REVERT: A 4569 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8740 (mp) REVERT: A 4694 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6276 (t0) REVERT: A 4695 ASP cc_start: 0.6173 (OUTLIER) cc_final: 0.5969 (p0) REVERT: A 4704 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9060 (mt) REVERT: A 4732 PHE cc_start: 0.7861 (m-80) cc_final: 0.7558 (m-80) REVERT: A 4879 MET cc_start: 0.9000 (tpt) cc_final: 0.8770 (tpt) REVERT: A 4993 MET cc_start: 0.8689 (ttm) cc_final: 0.8434 (ttm) REVERT: B 4245 MET cc_start: 0.8911 (mtt) cc_final: 0.8709 (mtt) REVERT: B 4569 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8742 (mp) REVERT: B 4694 ASP cc_start: 0.6791 (OUTLIER) cc_final: 0.6274 (t0) REVERT: B 4695 ASP cc_start: 0.6179 (OUTLIER) cc_final: 0.5973 (p0) REVERT: B 4704 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9058 (mt) REVERT: B 4732 PHE cc_start: 0.7864 (m-80) cc_final: 0.7559 (m-80) REVERT: B 4879 MET cc_start: 0.8998 (tpt) cc_final: 0.8768 (tpt) REVERT: B 4993 MET cc_start: 0.8688 (ttm) cc_final: 0.8438 (ttm) REVERT: C 4245 MET cc_start: 0.8911 (mtt) cc_final: 0.8710 (mtt) REVERT: C 4569 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8741 (mp) REVERT: C 4694 ASP cc_start: 0.6791 (OUTLIER) cc_final: 0.6275 (t0) REVERT: C 4695 ASP cc_start: 0.6169 (OUTLIER) cc_final: 0.5964 (p0) REVERT: C 4704 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9060 (mt) REVERT: C 4732 PHE cc_start: 0.7862 (m-80) cc_final: 0.7559 (m-80) REVERT: C 4879 MET cc_start: 0.8995 (tpt) cc_final: 0.8767 (tpt) REVERT: C 4993 MET cc_start: 0.8688 (ttm) cc_final: 0.8437 (ttm) REVERT: D 4245 MET cc_start: 0.8913 (mtt) cc_final: 0.8711 (mtt) REVERT: D 4569 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8737 (mp) REVERT: D 4694 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6278 (t0) REVERT: D 4695 ASP cc_start: 0.6173 (OUTLIER) cc_final: 0.5968 (p0) REVERT: D 4704 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9060 (mt) REVERT: D 4732 PHE cc_start: 0.7860 (m-80) cc_final: 0.7557 (m-80) REVERT: D 4879 MET cc_start: 0.8997 (tpt) cc_final: 0.8769 (tpt) REVERT: D 4993 MET cc_start: 0.8688 (ttm) cc_final: 0.8434 (ttm) outliers start: 44 outliers final: 12 residues processed: 376 average time/residue: 1.3613 time to fit residues: 574.5959 Evaluate side-chains 260 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain A residue 4695 ASP Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 3974 THR Chi-restraints excluded: chain B residue 4569 LEU Chi-restraints excluded: chain B residue 4694 ASP Chi-restraints excluded: chain B residue 4695 ASP Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 3974 THR Chi-restraints excluded: chain C residue 4569 LEU Chi-restraints excluded: chain C residue 4694 ASP Chi-restraints excluded: chain C residue 4695 ASP Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 3974 THR Chi-restraints excluded: chain D residue 4569 LEU Chi-restraints excluded: chain D residue 4694 ASP Chi-restraints excluded: chain D residue 4695 ASP Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4704 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4700 GLN A4997 ASN ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4700 GLN B4997 ASN ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4700 GLN C4997 ASN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4700 GLN D4997 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21060 Z= 0.190 Angle : 0.481 6.184 28420 Z= 0.264 Chirality : 0.037 0.117 3072 Planarity : 0.004 0.043 3604 Dihedral : 6.446 56.356 2752 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.90 % Allowed : 11.21 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 2472 helix: 2.31 (0.12), residues: 1752 sheet: -1.02 (0.51), residues: 112 loop : -0.77 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D4716 HIS 0.004 0.001 HIS B3994 PHE 0.015 0.001 PHE A4916 TYR 0.009 0.001 TYR A4994 ARG 0.005 0.000 ARG C4913 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 264 time to evaluate : 2.495 Fit side-chains REVERT: A 3974 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8379 (m) REVERT: A 4207 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.5945 (mpp) REVERT: A 4569 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8740 (mp) REVERT: A 4627 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.5393 (ttm) REVERT: A 4694 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6502 (t0) REVERT: A 4704 LEU cc_start: 0.9324 (mp) cc_final: 0.9009 (mt) REVERT: A 4839 MET cc_start: 0.8312 (tpp) cc_final: 0.7954 (tpp) REVERT: A 4879 MET cc_start: 0.8935 (tpt) cc_final: 0.8674 (tpt) REVERT: A 4887 MET cc_start: 0.8587 (mmm) cc_final: 0.8315 (mmm) REVERT: A 4993 MET cc_start: 0.8601 (ttm) cc_final: 0.8375 (ttm) REVERT: B 3974 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8381 (m) REVERT: B 4207 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.5945 (mpp) REVERT: B 4569 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8741 (mp) REVERT: B 4627 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5387 (ttm) REVERT: B 4694 ASP cc_start: 0.6782 (OUTLIER) cc_final: 0.6506 (t0) REVERT: B 4704 LEU cc_start: 0.9323 (mp) cc_final: 0.9007 (mt) REVERT: B 4879 MET cc_start: 0.8932 (tpt) cc_final: 0.8674 (tpt) REVERT: B 4887 MET cc_start: 0.8584 (mmm) cc_final: 0.8313 (mmm) REVERT: B 4993 MET cc_start: 0.8605 (ttm) cc_final: 0.8379 (ttm) REVERT: C 3974 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8381 (m) REVERT: C 4207 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.5947 (mpp) REVERT: C 4569 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8739 (mp) REVERT: C 4627 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5390 (ttm) REVERT: C 4694 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6506 (t0) REVERT: C 4704 LEU cc_start: 0.9324 (mp) cc_final: 0.9009 (mt) REVERT: C 4879 MET cc_start: 0.8929 (tpt) cc_final: 0.8677 (tpt) REVERT: C 4887 MET cc_start: 0.8583 (mmm) cc_final: 0.8312 (mmm) REVERT: C 4993 MET cc_start: 0.8600 (ttm) cc_final: 0.8373 (ttm) REVERT: D 3974 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8383 (m) REVERT: D 4207 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.5944 (mpp) REVERT: D 4569 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8738 (mp) REVERT: D 4627 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5390 (ttm) REVERT: D 4694 ASP cc_start: 0.6782 (OUTLIER) cc_final: 0.6507 (t0) REVERT: D 4704 LEU cc_start: 0.9326 (mp) cc_final: 0.9010 (mt) REVERT: D 4879 MET cc_start: 0.8932 (tpt) cc_final: 0.8677 (tpt) REVERT: D 4887 MET cc_start: 0.8585 (mmm) cc_final: 0.8311 (mmm) REVERT: D 4993 MET cc_start: 0.8600 (ttm) cc_final: 0.8375 (ttm) outliers start: 65 outliers final: 9 residues processed: 300 average time/residue: 1.2497 time to fit residues: 426.2476 Evaluate side-chains 265 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 236 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4207 MET Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4627 MET Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain A residue 4695 ASP Chi-restraints excluded: chain A residue 4816 ILE Chi-restraints excluded: chain B residue 3974 THR Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4569 LEU Chi-restraints excluded: chain B residue 4627 MET Chi-restraints excluded: chain B residue 4694 ASP Chi-restraints excluded: chain B residue 4695 ASP Chi-restraints excluded: chain B residue 4816 ILE Chi-restraints excluded: chain C residue 3974 THR Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4569 LEU Chi-restraints excluded: chain C residue 4627 MET Chi-restraints excluded: chain C residue 4694 ASP Chi-restraints excluded: chain C residue 4695 ASP Chi-restraints excluded: chain C residue 4816 ILE Chi-restraints excluded: chain D residue 3974 THR Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4569 LEU Chi-restraints excluded: chain D residue 4627 MET Chi-restraints excluded: chain D residue 4694 ASP Chi-restraints excluded: chain D residue 4695 ASP Chi-restraints excluded: chain D residue 4816 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 76 optimal weight: 0.0770 chunk 180 optimal weight: 8.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4997 ASN A5035 GLN ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4997 ASN B5035 GLN ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN C5035 GLN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4997 ASN D5035 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21060 Z= 0.182 Angle : 0.460 5.881 28420 Z= 0.251 Chirality : 0.037 0.129 3072 Planarity : 0.003 0.050 3604 Dihedral : 5.957 59.258 2734 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.88 % Allowed : 12.81 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 2.40 (0.17), residues: 2472 helix: 2.48 (0.12), residues: 1752 sheet: -0.96 (0.51), residues: 104 loop : -0.63 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D4716 HIS 0.003 0.001 HIS D4803 PHE 0.015 0.001 PHE B4916 TYR 0.011 0.001 TYR C4994 ARG 0.003 0.000 ARG D4913 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 248 time to evaluate : 2.295 Fit side-chains REVERT: A 3974 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8304 (m) REVERT: A 4039 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7657 (tmm) REVERT: A 4569 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8780 (mp) REVERT: A 4627 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5409 (ttm) REVERT: A 4672 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8303 (mtmt) REVERT: A 4704 LEU cc_start: 0.9310 (mp) cc_final: 0.8971 (mt) REVERT: A 4839 MET cc_start: 0.8196 (tpp) cc_final: 0.7950 (tpp) REVERT: A 5035 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: B 3974 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8305 (m) REVERT: B 4039 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7658 (tmm) REVERT: B 4569 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8779 (mp) REVERT: B 4627 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5401 (ttm) REVERT: B 4672 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8304 (mtmt) REVERT: B 4704 LEU cc_start: 0.9307 (mp) cc_final: 0.8969 (mt) REVERT: B 4839 MET cc_start: 0.8145 (tpp) cc_final: 0.7770 (tpp) REVERT: B 5035 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8311 (mt0) REVERT: C 3974 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8307 (m) REVERT: C 4039 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7661 (tmm) REVERT: C 4569 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8779 (mp) REVERT: C 4627 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.5404 (ttm) REVERT: C 4672 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8301 (mtmt) REVERT: C 4704 LEU cc_start: 0.9308 (mp) cc_final: 0.8968 (mt) REVERT: C 4839 MET cc_start: 0.8152 (tpp) cc_final: 0.7767 (tpp) REVERT: C 5035 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: D 3974 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8305 (m) REVERT: D 4039 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7656 (tmm) REVERT: D 4569 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8779 (mp) REVERT: D 4627 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.5399 (ttm) REVERT: D 4672 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8303 (mtmt) REVERT: D 4704 LEU cc_start: 0.9308 (mp) cc_final: 0.8969 (mt) REVERT: D 4839 MET cc_start: 0.8135 (tpp) cc_final: 0.7754 (tpp) REVERT: D 5035 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8316 (mt0) outliers start: 87 outliers final: 23 residues processed: 300 average time/residue: 1.2447 time to fit residues: 424.2281 Evaluate side-chains 279 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 236 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4039 MET Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4627 MET Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4705 VAL Chi-restraints excluded: chain A residue 4816 ILE Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 5035 GLN Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 3974 THR Chi-restraints excluded: chain B residue 4039 MET Chi-restraints excluded: chain B residue 4569 LEU Chi-restraints excluded: chain B residue 4627 MET Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4705 VAL Chi-restraints excluded: chain B residue 4816 ILE Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 5035 GLN Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 3974 THR Chi-restraints excluded: chain C residue 4039 MET Chi-restraints excluded: chain C residue 4569 LEU Chi-restraints excluded: chain C residue 4627 MET Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4705 VAL Chi-restraints excluded: chain C residue 4816 ILE Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 5035 GLN Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 3974 THR Chi-restraints excluded: chain D residue 4039 MET Chi-restraints excluded: chain D residue 4569 LEU Chi-restraints excluded: chain D residue 4627 MET Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4705 VAL Chi-restraints excluded: chain D residue 4816 ILE Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 5035 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 24 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4997 ASN A5035 GLN ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4997 ASN B5035 GLN ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN C5035 GLN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4997 ASN D5035 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21060 Z= 0.242 Angle : 0.485 6.591 28420 Z= 0.263 Chirality : 0.038 0.136 3072 Planarity : 0.004 0.059 3604 Dihedral : 4.666 52.429 2716 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.39 % Allowed : 12.99 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 2.35 (0.17), residues: 2472 helix: 2.44 (0.12), residues: 1752 sheet: -1.04 (0.51), residues: 104 loop : -0.61 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A4716 HIS 0.003 0.001 HIS D4803 PHE 0.019 0.001 PHE C4916 TYR 0.012 0.001 TYR B4994 ARG 0.002 0.000 ARG D4913 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 244 time to evaluate : 2.321 Fit side-chains REVERT: A 3974 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8369 (m) REVERT: A 4704 LEU cc_start: 0.9300 (mp) cc_final: 0.8957 (mt) REVERT: A 4839 MET cc_start: 0.8213 (tpp) cc_final: 0.7931 (tpp) REVERT: B 3974 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8371 (m) REVERT: B 4704 LEU cc_start: 0.9298 (mp) cc_final: 0.8956 (mt) REVERT: B 4839 MET cc_start: 0.8219 (tpp) cc_final: 0.7824 (tpp) REVERT: C 3974 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8373 (m) REVERT: C 4704 LEU cc_start: 0.9298 (mp) cc_final: 0.8956 (mt) REVERT: C 4839 MET cc_start: 0.8228 (tpp) cc_final: 0.7824 (tpp) REVERT: D 3974 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8370 (m) REVERT: D 4704 LEU cc_start: 0.9300 (mp) cc_final: 0.8957 (mt) REVERT: D 4839 MET cc_start: 0.8209 (tpp) cc_final: 0.7813 (tpp) outliers start: 76 outliers final: 32 residues processed: 280 average time/residue: 1.2829 time to fit residues: 408.0046 Evaluate side-chains 256 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4627 MET Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4705 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4816 ILE Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain B residue 3974 THR Chi-restraints excluded: chain B residue 4569 LEU Chi-restraints excluded: chain B residue 4627 MET Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4705 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4816 ILE Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain C residue 3974 THR Chi-restraints excluded: chain C residue 4569 LEU Chi-restraints excluded: chain C residue 4627 MET Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4705 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4816 ILE Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain D residue 3974 THR Chi-restraints excluded: chain D residue 4569 LEU Chi-restraints excluded: chain D residue 4627 MET Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4705 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4816 ILE Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4911 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4997 ASN A5035 GLN ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4997 ASN B5035 GLN ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN C5035 GLN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4997 ASN D5035 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21060 Z= 0.197 Angle : 0.466 7.151 28420 Z= 0.251 Chirality : 0.037 0.131 3072 Planarity : 0.004 0.055 3604 Dihedral : 4.556 52.258 2716 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.75 % Allowed : 13.53 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 2.39 (0.17), residues: 2472 helix: 2.48 (0.12), residues: 1756 sheet: -1.03 (0.50), residues: 104 loop : -0.66 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C4716 HIS 0.003 0.001 HIS D4803 PHE 0.016 0.001 PHE D4916 TYR 0.027 0.001 TYR A4687 ARG 0.002 0.000 ARG B4188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 228 time to evaluate : 2.238 Fit side-chains REVERT: A 4569 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8771 (mp) REVERT: A 4627 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5676 (ttm) REVERT: A 4704 LEU cc_start: 0.9304 (mp) cc_final: 0.8959 (mt) REVERT: A 4707 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8508 (m-40) REVERT: A 4839 MET cc_start: 0.8189 (tpp) cc_final: 0.7937 (tpp) REVERT: B 4569 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8771 (mp) REVERT: B 4627 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5670 (ttm) REVERT: B 4704 LEU cc_start: 0.9302 (mp) cc_final: 0.8957 (mt) REVERT: B 4707 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8509 (m-40) REVERT: B 4839 MET cc_start: 0.8230 (tpp) cc_final: 0.7824 (tpp) REVERT: C 4569 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8771 (mp) REVERT: C 4627 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5668 (ttm) REVERT: C 4704 LEU cc_start: 0.9304 (mp) cc_final: 0.8958 (mt) REVERT: C 4707 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8508 (m-40) REVERT: C 4839 MET cc_start: 0.8239 (tpp) cc_final: 0.7828 (tpp) REVERT: D 4569 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8770 (mp) REVERT: D 4627 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5663 (ttm) REVERT: D 4704 LEU cc_start: 0.9303 (mp) cc_final: 0.8957 (mt) REVERT: D 4707 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8505 (m-40) REVERT: D 4839 MET cc_start: 0.8222 (tpp) cc_final: 0.7818 (tpp) outliers start: 84 outliers final: 24 residues processed: 280 average time/residue: 1.3084 time to fit residues: 414.5837 Evaluate side-chains 248 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 212 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4627 MET Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4705 VAL Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4816 ILE Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain B residue 4569 LEU Chi-restraints excluded: chain B residue 4627 MET Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4705 VAL Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4816 ILE Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain C residue 4569 LEU Chi-restraints excluded: chain C residue 4627 MET Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4705 VAL Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4816 ILE Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain D residue 4569 LEU Chi-restraints excluded: chain D residue 4627 MET Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4705 VAL Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4816 ILE Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4911 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 111 optimal weight: 0.0030 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4997 ASN A5035 GLN ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4997 ASN B5035 GLN ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN C5035 GLN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4997 ASN D5035 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21060 Z= 0.149 Angle : 0.452 7.621 28420 Z= 0.243 Chirality : 0.036 0.138 3072 Planarity : 0.003 0.049 3604 Dihedral : 4.416 50.572 2712 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.26 % Allowed : 14.20 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 2.55 (0.17), residues: 2472 helix: 2.62 (0.12), residues: 1756 sheet: -0.93 (0.50), residues: 104 loop : -0.65 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C4716 HIS 0.002 0.001 HIS A3994 PHE 0.013 0.001 PHE D4916 TYR 0.023 0.001 TYR A4687 ARG 0.003 0.000 ARG D4188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 236 time to evaluate : 2.572 Fit side-chains REVERT: A 4627 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5619 (ttm) REVERT: A 4704 LEU cc_start: 0.9293 (mp) cc_final: 0.8966 (mt) REVERT: A 4839 MET cc_start: 0.8151 (tpp) cc_final: 0.7775 (mmp) REVERT: A 4844 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8760 (tp) REVERT: A 4887 MET cc_start: 0.8542 (mmm) cc_final: 0.8195 (mmm) REVERT: A 5031 GLN cc_start: 0.8547 (tt0) cc_final: 0.8205 (tt0) REVERT: B 4627 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5610 (ttm) REVERT: B 4704 LEU cc_start: 0.9290 (mp) cc_final: 0.8965 (mt) REVERT: B 4839 MET cc_start: 0.8140 (tpp) cc_final: 0.7810 (tpp) REVERT: B 4844 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8764 (tp) REVERT: B 4887 MET cc_start: 0.8536 (mmm) cc_final: 0.8192 (mmm) REVERT: B 5031 GLN cc_start: 0.8549 (tt0) cc_final: 0.8204 (tt0) REVERT: C 4627 MET cc_start: 0.6207 (OUTLIER) cc_final: 0.5611 (ttm) REVERT: C 4704 LEU cc_start: 0.9293 (mp) cc_final: 0.8963 (mt) REVERT: C 4839 MET cc_start: 0.8147 (tpp) cc_final: 0.7811 (tpp) REVERT: C 4844 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8758 (tp) REVERT: C 4887 MET cc_start: 0.8540 (mmm) cc_final: 0.8195 (mmm) REVERT: C 5031 GLN cc_start: 0.8550 (tt0) cc_final: 0.8204 (tt0) REVERT: D 4627 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5608 (ttm) REVERT: D 4704 LEU cc_start: 0.9291 (mp) cc_final: 0.8962 (mt) REVERT: D 4839 MET cc_start: 0.8128 (tpp) cc_final: 0.7802 (tpp) REVERT: D 4844 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8764 (tp) REVERT: D 4887 MET cc_start: 0.8538 (mmm) cc_final: 0.8192 (mmm) REVERT: D 5031 GLN cc_start: 0.8546 (tt0) cc_final: 0.8204 (tt0) outliers start: 73 outliers final: 24 residues processed: 276 average time/residue: 1.3421 time to fit residues: 419.4976 Evaluate side-chains 252 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 220 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4627 MET Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4816 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4627 MET Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4816 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4627 MET Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4816 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4627 MET Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4816 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4911 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: