Starting phenix.real_space_refine on Mon Mar 18 10:53:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sf0_40435/03_2024/8sf0_40435_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sf0_40435/03_2024/8sf0_40435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sf0_40435/03_2024/8sf0_40435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sf0_40435/03_2024/8sf0_40435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sf0_40435/03_2024/8sf0_40435_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sf0_40435/03_2024/8sf0_40435_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4 5.49 5 S 160 5.16 5 C 13432 2.51 5 N 3288 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4196": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A GLU 4206": "OE1" <-> "OE2" Residue "A GLU 4212": "OE1" <-> "OE2" Residue "A PHE 4219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4229": "OE1" <-> "OE2" Residue "A TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4726": "OD1" <-> "OD2" Residue "A ASP 4917": "OD1" <-> "OD2" Residue "A ASP 4966": "OD1" <-> "OD2" Residue "A PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 5026": "OD1" <-> "OD2" Residue "A TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4196": "OE1" <-> "OE2" Residue "B GLU 4199": "OE1" <-> "OE2" Residue "B GLU 4206": "OE1" <-> "OE2" Residue "B GLU 4212": "OE1" <-> "OE2" Residue "B PHE 4219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4229": "OE1" <-> "OE2" Residue "B TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4726": "OD1" <-> "OD2" Residue "B ASP 4917": "OD1" <-> "OD2" Residue "B ASP 4966": "OD1" <-> "OD2" Residue "B PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4196": "OE1" <-> "OE2" Residue "C GLU 4199": "OE1" <-> "OE2" Residue "C GLU 4206": "OE1" <-> "OE2" Residue "C GLU 4212": "OE1" <-> "OE2" Residue "C PHE 4219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4229": "OE1" <-> "OE2" Residue "C TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4726": "OD1" <-> "OD2" Residue "C ASP 4917": "OD1" <-> "OD2" Residue "C ASP 4966": "OD1" <-> "OD2" Residue "C PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 5026": "OD1" <-> "OD2" Residue "C TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4196": "OE1" <-> "OE2" Residue "D GLU 4199": "OE1" <-> "OE2" Residue "D GLU 4206": "OE1" <-> "OE2" Residue "D GLU 4212": "OE1" <-> "OE2" Residue "D PHE 4219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4229": "OE1" <-> "OE2" Residue "D TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4726": "OD1" <-> "OD2" Residue "D ASP 4917": "OD1" <-> "OD2" Residue "D ASP 4966": "OD1" <-> "OD2" Residue "D PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 5026": "OD1" <-> "OD2" Residue "D TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20664 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: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4469 SG CYS A4958 55.702 81.546 88.347 1.00 47.31 S ATOM 4494 SG CYS A4961 58.158 82.398 91.197 1.00 45.93 S ATOM 9612 SG CYS B4958 60.133 55.703 88.347 1.00 47.35 S ATOM 9637 SG CYS B4961 59.282 58.157 91.198 1.00 45.70 S ATOM 14755 SG CYS C4958 85.978 60.133 88.347 1.00 47.42 S ATOM 14780 SG CYS C4961 83.523 59.282 91.197 1.00 45.49 S ATOM 19898 SG CYS D4958 81.547 85.978 88.347 1.00 47.46 S ATOM 19923 SG CYS D4961 82.398 83.522 91.198 1.00 46.04 S Time building chain proxies: 10.53, per 1000 atoms: 0.51 Number of scatterers: 20664 At special positions: 0 Unit cell: (142.968, 142.968, 131.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 160 16.00 P 4 15.00 O 3776 8.00 N 3288 7.00 C 13432 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: 7.71 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 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... running ksdssp... Secondary structure from input PDB file: 132 helices and 8 sheets defined 70.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 3951 through 3969 removed outlier: 3.575A pdb=" N ALA A3958 " --> pdb=" O ALA A3954 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A3960 " --> pdb=" O SER A3956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3974 through 3982 removed outlier: 3.690A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4005 removed outlier: 3.523A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) Processing helix chain 'A' and resid 4011 through 4031 removed outlier: 3.629A pdb=" N ASP A4018 " --> pdb=" O LYS A4014 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A4019 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A4020 " --> pdb=" O LEU A4016 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A4021 " --> pdb=" O LEU A4017 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A4025 " --> pdb=" O LYS A4021 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A4026 " --> pdb=" O ASP A4022 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4050 Processing helix chain 'A' and resid 4052 through 4055 No H-bonds generated for 'chain 'A' and resid 4052 through 4055' Processing helix chain 'A' and resid 4199 through 4206 Processing helix chain 'A' and resid 4208 through 4223 Processing helix chain 'A' and resid 4227 through 4251 removed outlier: 4.429A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4541 through 4557 Processing helix chain 'A' and resid 4559 through 4579 removed outlier: 4.336A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4639 through 4664 removed outlier: 3.776A pdb=" N TRP A4644 " --> pdb=" O GLU A4640 " (cutoff:3.500A) Processing helix chain 'A' and resid 4666 through 4682 Processing helix chain 'A' and resid 4697 through 4706 removed outlier: 3.728A pdb=" N ARG A4703 " --> pdb=" O GLY A4699 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) Processing helix chain 'A' and resid 4720 through 4732 removed outlier: 4.723A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4734 through 4741 Processing helix chain 'A' and resid 4745 through 4749 removed outlier: 4.153A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4745 through 4749' Processing helix chain 'A' and resid 4773 through 4785 removed outlier: 3.583A pdb=" N THR A4785 " --> pdb=" O GLY A4781 " (cutoff:3.500A) Processing helix chain 'A' and resid 4787 through 4804 removed outlier: 3.852A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4819 removed outlier: 3.569A pdb=" N LEU A4814 " --> pdb=" O ALA A4811 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.656A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4834 through 4858 removed outlier: 3.565A pdb=" N ASN A4857 " --> pdb=" O VAL A4853 " (cutoff:3.500A) Processing helix chain 'A' and resid 4860 through 4862 No H-bonds generated for 'chain 'A' and resid 4860 through 4862' Processing helix chain 'A' and resid 4879 through 4889 Processing helix chain 'A' and resid 4896 through 4899 Processing helix chain 'A' and resid 4910 through 4923 Processing helix chain 'A' and resid 4927 through 4956 Processing helix chain 'A' and resid 4965 through 4970 removed outlier: 4.282A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4974 through 4981 Processing helix chain 'A' and resid 4985 through 4997 Processing helix chain 'A' and resid 5005 through 5015 Processing helix chain 'A' and resid 5028 through 5031 No H-bonds generated for 'chain 'A' and resid 5028 through 5031' Processing helix chain 'A' and resid 5033 through 5036 No H-bonds generated for 'chain 'A' and resid 5033 through 5036' Processing helix chain 'B' and resid 3951 through 3969 removed outlier: 3.575A pdb=" N ALA B3958 " --> pdb=" O ALA B3954 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3974 through 3982 removed outlier: 3.690A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4005 removed outlier: 3.522A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) Processing helix chain 'B' and resid 4011 through 4031 removed outlier: 3.629A pdb=" N ASP B4018 " --> pdb=" O LYS B4014 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B4019 " --> pdb=" O GLU B4015 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN B4020 " --> pdb=" O LEU B4016 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B4021 " --> pdb=" O LEU B4017 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B4025 " --> pdb=" O LYS B4021 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET B4026 " --> pdb=" O ASP B4022 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4050 Processing helix chain 'B' and resid 4052 through 4055 No H-bonds generated for 'chain 'B' and resid 4052 through 4055' Processing helix chain 'B' and resid 4199 through 4206 Processing helix chain 'B' and resid 4208 through 4223 Processing helix chain 'B' and resid 4227 through 4251 removed outlier: 4.430A pdb=" N MET B4231 " --> pdb=" O GLU B4227 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU B4232 " --> pdb=" O ALA B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4541 through 4557 Processing helix chain 'B' and resid 4559 through 4579 removed outlier: 4.336A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4639 through 4664 removed outlier: 3.776A pdb=" N TRP B4644 " --> pdb=" O GLU B4640 " (cutoff:3.500A) Processing helix chain 'B' and resid 4666 through 4682 Processing helix chain 'B' and resid 4697 through 4706 removed outlier: 3.730A pdb=" N ARG B4703 " --> pdb=" O GLY B4699 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) Processing helix chain 'B' and resid 4720 through 4732 removed outlier: 4.723A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4734 through 4741 Processing helix chain 'B' and resid 4745 through 4749 removed outlier: 4.153A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4745 through 4749' Processing helix chain 'B' and resid 4773 through 4785 removed outlier: 3.583A pdb=" N THR B4785 " --> pdb=" O GLY B4781 " (cutoff:3.500A) Processing helix chain 'B' and resid 4787 through 4804 removed outlier: 3.853A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4819 removed outlier: 3.569A pdb=" N LEU B4814 " --> pdb=" O ALA B4811 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.656A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4834 through 4858 removed outlier: 3.563A pdb=" N ASN B4857 " --> pdb=" O VAL B4853 " (cutoff:3.500A) Processing helix chain 'B' and resid 4860 through 4862 No H-bonds generated for 'chain 'B' and resid 4860 through 4862' Processing helix chain 'B' and resid 4879 through 4889 Processing helix chain 'B' and resid 4896 through 4899 Processing helix chain 'B' and resid 4910 through 4923 Processing helix chain 'B' and resid 4927 through 4956 Processing helix chain 'B' and resid 4965 through 4970 removed outlier: 4.282A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4974 through 4981 Processing helix chain 'B' and resid 4985 through 4997 Processing helix chain 'B' and resid 5005 through 5015 Processing helix chain 'B' and resid 5028 through 5031 No H-bonds generated for 'chain 'B' and resid 5028 through 5031' Processing helix chain 'B' and resid 5033 through 5036 No H-bonds generated for 'chain 'B' and resid 5033 through 5036' Processing helix chain 'C' and resid 3951 through 3969 removed outlier: 3.575A pdb=" N ALA C3958 " --> pdb=" O ALA C3954 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C3960 " --> pdb=" O SER C3956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3974 through 3982 removed outlier: 3.690A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) Processing helix chain 'C' and resid 3985 through 4005 removed outlier: 3.522A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) Processing helix chain 'C' and resid 4011 through 4031 removed outlier: 3.629A pdb=" N ASP C4018 " --> pdb=" O LYS C4014 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C4019 " --> pdb=" O GLU C4015 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN C4020 " --> pdb=" O LEU C4016 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C4021 " --> pdb=" O LEU C4017 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C4025 " --> pdb=" O LYS C4021 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C4026 " --> pdb=" O ASP C4022 " (cutoff:3.500A) Processing helix chain 'C' and resid 4039 through 4050 Processing helix chain 'C' and resid 4052 through 4055 No H-bonds generated for 'chain 'C' and resid 4052 through 4055' Processing helix chain 'C' and resid 4199 through 4206 Processing helix chain 'C' and resid 4208 through 4223 Processing helix chain 'C' and resid 4227 through 4251 removed outlier: 4.429A pdb=" N MET C4231 " --> pdb=" O GLU C4227 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4541 through 4557 Processing helix chain 'C' and resid 4559 through 4579 removed outlier: 4.336A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4639 through 4664 removed outlier: 3.777A pdb=" N TRP C4644 " --> pdb=" O GLU C4640 " (cutoff:3.500A) Processing helix chain 'C' and resid 4666 through 4682 Processing helix chain 'C' and resid 4697 through 4706 removed outlier: 3.730A pdb=" N ARG C4703 " --> pdb=" O GLY C4699 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) Processing helix chain 'C' and resid 4720 through 4732 removed outlier: 4.723A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4734 through 4741 Processing helix chain 'C' and resid 4745 through 4749 removed outlier: 4.153A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4745 through 4749' Processing helix chain 'C' and resid 4773 through 4785 removed outlier: 3.583A pdb=" N THR C4785 " --> pdb=" O GLY C4781 " (cutoff:3.500A) Processing helix chain 'C' and resid 4787 through 4804 removed outlier: 3.853A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4819 removed outlier: 3.568A pdb=" N LEU C4814 " --> pdb=" O ALA C4811 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.656A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4834 through 4858 removed outlier: 3.562A pdb=" N ASN C4857 " --> pdb=" O VAL C4853 " (cutoff:3.500A) Processing helix chain 'C' and resid 4860 through 4862 No H-bonds generated for 'chain 'C' and resid 4860 through 4862' Processing helix chain 'C' and resid 4879 through 4889 Processing helix chain 'C' and resid 4896 through 4899 Processing helix chain 'C' and resid 4910 through 4923 Processing helix chain 'C' and resid 4927 through 4956 Processing helix chain 'C' and resid 4965 through 4970 removed outlier: 4.282A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4974 through 4981 Processing helix chain 'C' and resid 4985 through 4997 Processing helix chain 'C' and resid 5005 through 5015 Processing helix chain 'C' and resid 5028 through 5031 No H-bonds generated for 'chain 'C' and resid 5028 through 5031' Processing helix chain 'C' and resid 5033 through 5036 No H-bonds generated for 'chain 'C' and resid 5033 through 5036' Processing helix chain 'D' and resid 3951 through 3969 removed outlier: 3.575A pdb=" N ALA D3958 " --> pdb=" O ALA D3954 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D3960 " --> pdb=" O SER D3956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3974 through 3982 removed outlier: 3.690A pdb=" N HIS D3982 " --> pdb=" O GLN D3978 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4005 removed outlier: 3.523A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) Processing helix chain 'D' and resid 4011 through 4031 removed outlier: 3.629A pdb=" N ASP D4018 " --> pdb=" O LYS D4014 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D4019 " --> pdb=" O GLU D4015 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D4020 " --> pdb=" O LEU D4016 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D4021 " --> pdb=" O LEU D4017 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D4025 " --> pdb=" O LYS D4021 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D4026 " --> pdb=" O ASP D4022 " (cutoff:3.500A) Processing helix chain 'D' and resid 4039 through 4050 Processing helix chain 'D' and resid 4052 through 4055 No H-bonds generated for 'chain 'D' and resid 4052 through 4055' Processing helix chain 'D' and resid 4199 through 4206 Processing helix chain 'D' and resid 4208 through 4223 Processing helix chain 'D' and resid 4227 through 4251 removed outlier: 4.429A pdb=" N MET D4231 " --> pdb=" O GLU D4227 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLU D4232 " --> pdb=" O ALA D4228 " (cutoff:3.500A) Processing helix chain 'D' and resid 4541 through 4557 Processing helix chain 'D' and resid 4559 through 4579 removed outlier: 4.336A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4639 through 4664 removed outlier: 3.779A pdb=" N TRP D4644 " --> pdb=" O GLU D4640 " (cutoff:3.500A) Processing helix chain 'D' and resid 4666 through 4682 Processing helix chain 'D' and resid 4697 through 4706 removed outlier: 3.730A pdb=" N ARG D4703 " --> pdb=" O GLY D4699 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) Processing helix chain 'D' and resid 4720 through 4732 removed outlier: 4.723A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4734 through 4741 Processing helix chain 'D' and resid 4745 through 4749 removed outlier: 4.153A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4745 through 4749' Processing helix chain 'D' and resid 4773 through 4785 removed outlier: 3.584A pdb=" N THR D4785 " --> pdb=" O GLY D4781 " (cutoff:3.500A) Processing helix chain 'D' and resid 4787 through 4804 removed outlier: 3.852A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4819 removed outlier: 3.571A pdb=" N LEU D4814 " --> pdb=" O ALA D4811 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.656A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4834 through 4858 removed outlier: 3.561A pdb=" N ASN D4857 " --> pdb=" O VAL D4853 " (cutoff:3.500A) Processing helix chain 'D' and resid 4860 through 4862 No H-bonds generated for 'chain 'D' and resid 4860 through 4862' Processing helix chain 'D' and resid 4879 through 4889 Processing helix chain 'D' and resid 4896 through 4899 Processing helix chain 'D' and resid 4910 through 4923 Processing helix chain 'D' and resid 4927 through 4956 Processing helix chain 'D' and resid 4965 through 4970 removed outlier: 4.282A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4974 through 4981 Processing helix chain 'D' and resid 4985 through 4997 Processing helix chain 'D' and resid 5005 through 5015 Processing helix chain 'D' and resid 5028 through 5031 No H-bonds generated for 'chain 'D' and resid 5028 through 5031' Processing helix chain 'D' and resid 5033 through 5036 No H-bonds generated for 'chain 'D' and resid 5033 through 5036' Processing sheet with id= A, first strand: chain 'A' and resid 4178 through 4184 Processing sheet with id= B, first strand: chain 'A' and resid 4580 through 4583 Processing sheet with id= C, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id= D, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id= E, first strand: chain 'C' and resid 4178 through 4184 Processing sheet with id= F, first strand: chain 'C' and resid 4580 through 4583 Processing sheet with id= G, first strand: chain 'D' and resid 4178 through 4184 Processing sheet with id= H, first strand: chain 'D' and resid 4580 through 4583 1172 hydrogen bonds defined for protein. 3372 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: 6.50 Time building geometry restraints manager: 8.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6479 1.34 - 1.46: 4267 1.46 - 1.58: 10130 1.58 - 1.69: 8 1.69 - 1.81: 276 Bond restraints: 21160 Sorted by residual: bond pdb=" C4 CMP D5101 " pdb=" C5 CMP D5101 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" C3' CMP B5101 " pdb=" C4' CMP B5101 " ideal model delta sigma weight residual 1.521 1.505 0.016 1.50e-02 4.44e+03 1.15e+00 bond pdb=" C3' CMP A5101 " pdb=" C4' CMP A5101 " ideal model delta sigma weight residual 1.521 1.505 0.016 1.50e-02 4.44e+03 1.15e+00 bond pdb=" C3' CMP D5101 " pdb=" C4' CMP D5101 " ideal model delta sigma weight residual 1.521 1.505 0.016 1.50e-02 4.44e+03 1.15e+00 bond pdb=" C4 CMP A5101 " pdb=" C5 CMP A5101 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.14e+00 ... (remaining 21155 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.41: 446 106.41 - 113.77: 11491 113.77 - 121.14: 12003 121.14 - 128.50: 4484 128.50 - 135.86: 152 Bond angle restraints: 28576 Sorted by residual: angle pdb=" N GLU B4676 " pdb=" CA GLU B4676 " pdb=" CB GLU B4676 " ideal model delta sigma weight residual 110.16 115.18 -5.02 1.48e+00 4.57e-01 1.15e+01 angle pdb=" N GLU D4676 " pdb=" CA GLU D4676 " pdb=" CB GLU D4676 " ideal model delta sigma weight residual 110.16 115.12 -4.96 1.48e+00 4.57e-01 1.12e+01 angle pdb=" N GLU C4676 " pdb=" CA GLU C4676 " pdb=" CB GLU C4676 " ideal model delta sigma weight residual 110.16 115.12 -4.96 1.48e+00 4.57e-01 1.12e+01 angle pdb=" N GLU A4676 " pdb=" CA GLU A4676 " pdb=" CB GLU A4676 " ideal model delta sigma weight residual 110.16 115.11 -4.95 1.48e+00 4.57e-01 1.12e+01 angle pdb=" CA GLU C4676 " pdb=" CB GLU C4676 " pdb=" CG GLU C4676 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.45e+00 ... (remaining 28571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.74: 12172 32.74 - 65.48: 228 65.48 - 98.22: 24 98.22 - 130.96: 4 130.96 - 163.70: 12 Dihedral angle restraints: 12440 sinusoidal: 5104 harmonic: 7336 Sorted by residual: dihedral pdb=" C3' CMP B5101 " pdb=" O3' CMP B5101 " pdb=" P CMP B5101 " pdb=" O1P CMP B5101 " ideal model delta sinusoidal sigma weight residual -60.00 99.68 -159.68 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C3' CMP A5101 " pdb=" O3' CMP A5101 " pdb=" P CMP A5101 " pdb=" O1P CMP A5101 " ideal model delta sinusoidal sigma weight residual -60.00 99.66 -159.66 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C3' CMP C5101 " pdb=" O3' CMP C5101 " pdb=" P CMP C5101 " pdb=" O1P CMP C5101 " ideal model delta sinusoidal sigma weight residual -60.00 99.66 -159.66 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 12437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2128 0.035 - 0.070: 805 0.070 - 0.105: 127 0.105 - 0.140: 24 0.140 - 0.175: 8 Chirality restraints: 3092 Sorted by residual: chirality pdb=" CB VAL B4853 " pdb=" CA VAL B4853 " pdb=" CG1 VAL B4853 " pdb=" CG2 VAL B4853 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CB VAL D4853 " pdb=" CA VAL D4853 " pdb=" CG1 VAL D4853 " pdb=" CG2 VAL D4853 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CB VAL C4853 " pdb=" CA VAL C4853 " pdb=" CG1 VAL C4853 " pdb=" CG2 VAL C4853 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 3089 not shown) Planarity restraints: 3604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D3971 " -0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO D3972 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D3972 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D3972 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A3971 " -0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A3972 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A3972 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A3972 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B3971 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B3972 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B3972 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B3972 " 0.045 5.00e-02 4.00e+02 ... (remaining 3601 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 395 2.71 - 3.26: 21489 3.26 - 3.80: 34275 3.80 - 4.35: 43078 4.35 - 4.90: 71816 Nonbonded interactions: 171053 Sorted by model distance: nonbonded pdb=" OH TYR B4967 " pdb=" OE2 GLU B5033 " model vdw 2.161 2.440 nonbonded pdb=" OH TYR D4967 " pdb=" OE2 GLU D5033 " model vdw 2.161 2.440 nonbonded pdb=" OH TYR C4967 " pdb=" OE2 GLU C5033 " model vdw 2.162 2.440 nonbonded pdb=" OH TYR A4967 " pdb=" OE2 GLU A5033 " model vdw 2.162 2.440 nonbonded pdb=" OE1 GLU A4232 " pdb=" NE1 TRP A5019 " model vdw 2.272 2.520 ... (remaining 171048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 6.760 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: 0.010 Extract box with map and model: 14.540 Check model and map are aligned: 0.300 Set scattering table: 0.150 Process input model: 57.720 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.120 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 0.029 21160 Z= 0.188 Angle : 0.505 5.835 28576 Z= 0.275 Chirality : 0.037 0.175 3092 Planarity : 0.004 0.082 3604 Dihedral : 15.098 163.705 7700 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.75 (0.17), residues: 2472 helix: 1.87 (0.12), residues: 1724 sheet: 0.55 (0.52), residues: 104 loop : -0.66 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D4644 HIS 0.004 0.001 HIS D4803 PHE 0.017 0.001 PHE A4683 TYR 0.012 0.001 TYR B5032 ARG 0.003 0.000 ARG D4202 *********************** 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 372 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.212 Fit side-chains REVERT: A 4043 GLN cc_start: 0.8272 (mm110) cc_final: 0.7683 (mm110) REVERT: A 4633 GLU cc_start: 0.6843 (tp30) cc_final: 0.6570 (pp20) REVERT: A 4851 TYR cc_start: 0.8835 (m-80) cc_final: 0.8625 (m-80) REVERT: A 4980 LEU cc_start: 0.8247 (mt) cc_final: 0.7850 (tp) REVERT: B 4043 GLN cc_start: 0.8272 (mm110) cc_final: 0.7686 (mm110) REVERT: B 4633 GLU cc_start: 0.6826 (tp30) cc_final: 0.6607 (pp20) REVERT: B 4851 TYR cc_start: 0.8726 (m-80) cc_final: 0.8517 (m-80) REVERT: B 4980 LEU cc_start: 0.8237 (mt) cc_final: 0.7842 (tp) REVERT: C 4043 GLN cc_start: 0.8268 (mm110) cc_final: 0.7684 (mm110) REVERT: C 4633 GLU cc_start: 0.6814 (tp30) cc_final: 0.6600 (pp20) REVERT: C 4980 LEU cc_start: 0.8249 (mt) cc_final: 0.7853 (tp) REVERT: D 4043 GLN cc_start: 0.8270 (mm110) cc_final: 0.7678 (mm110) REVERT: D 4633 GLU cc_start: 0.6829 (tp30) cc_final: 0.6593 (pp20) REVERT: D 4980 LEU cc_start: 0.8245 (mt) cc_final: 0.7851 (tp) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 1.6090 time to fit residues: 660.8593 Evaluate side-chains 301 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.265 ------------------------------------------------------------------------------- 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: 6.9990 chunk 104 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3998 HIS A4223 ASN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4662 ASN ** B3982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3998 HIS B4223 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4662 ASN ** C3982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3998 HIS C4223 ASN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4662 ASN C4997 ASN ** D3982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3998 HIS D4223 ASN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4662 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21160 Z= 0.284 Angle : 0.564 7.538 28576 Z= 0.295 Chirality : 0.037 0.122 3092 Planarity : 0.005 0.060 3604 Dihedral : 12.280 163.165 2748 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.14 % Allowed : 8.44 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2472 helix: 1.89 (0.12), residues: 1668 sheet: 0.11 (0.50), residues: 104 loop : -0.25 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C4716 HIS 0.004 0.001 HIS A5003 PHE 0.015 0.002 PHE B4916 TYR 0.013 0.002 TYR D4580 ARG 0.008 0.001 ARG D4736 *********************** 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 353 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 305 time to evaluate : 2.219 Fit side-chains REVERT: A 3955 MET cc_start: 0.6240 (ttm) cc_final: 0.5981 (ttm) REVERT: A 3999 MET cc_start: 0.6710 (mmm) cc_final: 0.6482 (mmp) REVERT: A 4043 GLN cc_start: 0.8217 (mm110) cc_final: 0.7694 (mm-40) REVERT: A 4204 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6990 (mt0) REVERT: A 4633 GLU cc_start: 0.6844 (tp30) cc_final: 0.6470 (pp20) REVERT: A 4911 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7575 (mm) REVERT: A 4980 LEU cc_start: 0.8359 (mt) cc_final: 0.7862 (tp) REVERT: A 5027 CYS cc_start: 0.8072 (p) cc_final: 0.7804 (p) REVERT: B 3955 MET cc_start: 0.6232 (ttm) cc_final: 0.5969 (ttm) REVERT: B 3999 MET cc_start: 0.6728 (mmm) cc_final: 0.6502 (mmp) REVERT: B 4043 GLN cc_start: 0.8215 (mm110) cc_final: 0.7692 (mm-40) REVERT: B 4204 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6990 (mt0) REVERT: B 4633 GLU cc_start: 0.6827 (tp30) cc_final: 0.6509 (pp20) REVERT: B 4911 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7569 (mm) REVERT: B 4980 LEU cc_start: 0.8356 (mt) cc_final: 0.7856 (tp) REVERT: B 5027 CYS cc_start: 0.8072 (p) cc_final: 0.7805 (p) REVERT: C 3955 MET cc_start: 0.6239 (ttm) cc_final: 0.5980 (ttm) REVERT: C 3999 MET cc_start: 0.6724 (mmm) cc_final: 0.6499 (mmp) REVERT: C 4043 GLN cc_start: 0.8211 (mm110) cc_final: 0.7688 (mm-40) REVERT: C 4204 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6986 (mt0) REVERT: C 4633 GLU cc_start: 0.6818 (tp30) cc_final: 0.6500 (pp20) REVERT: C 4911 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7566 (mm) REVERT: C 4980 LEU cc_start: 0.8363 (mt) cc_final: 0.7867 (tp) REVERT: C 5027 CYS cc_start: 0.8078 (p) cc_final: 0.7817 (p) REVERT: D 3955 MET cc_start: 0.6249 (ttm) cc_final: 0.5989 (ttm) REVERT: D 3999 MET cc_start: 0.6712 (mmm) cc_final: 0.6485 (mmp) REVERT: D 4043 GLN cc_start: 0.8215 (mm110) cc_final: 0.7684 (mm-40) REVERT: D 4204 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6992 (mt0) REVERT: D 4633 GLU cc_start: 0.6835 (tp30) cc_final: 0.6495 (pp20) REVERT: D 4911 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7561 (mm) REVERT: D 4980 LEU cc_start: 0.8357 (mt) cc_final: 0.7864 (tp) REVERT: D 5027 CYS cc_start: 0.8073 (p) cc_final: 0.7811 (p) outliers start: 48 outliers final: 12 residues processed: 321 average time/residue: 1.4704 time to fit residues: 527.2533 Evaluate side-chains 321 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 301 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3987 ASP Chi-restraints excluded: chain A residue 4204 GLN Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 3987 ASP Chi-restraints excluded: chain B residue 4204 GLN Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 3987 ASP Chi-restraints excluded: chain C residue 4204 GLN Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 3987 ASP Chi-restraints excluded: chain D residue 4204 GLN Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 153 optimal weight: 0.0270 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 180 optimal weight: 0.0030 overall best weight: 0.7450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3978 GLN A3982 HIS A4223 ASN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 GLN B3978 GLN B3982 HIS B4223 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4933 GLN C3978 GLN C3982 HIS C4223 ASN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 GLN D3978 GLN D3982 HIS ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21160 Z= 0.177 Angle : 0.483 7.529 28576 Z= 0.254 Chirality : 0.035 0.129 3092 Planarity : 0.004 0.045 3604 Dihedral : 12.164 163.467 2748 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.43 % Allowed : 9.46 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.17), residues: 2472 helix: 2.07 (0.12), residues: 1664 sheet: 0.18 (0.50), residues: 104 loop : -0.17 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D4644 HIS 0.003 0.001 HIS C3998 PHE 0.012 0.001 PHE A4916 TYR 0.010 0.001 TYR B4994 ARG 0.006 0.000 ARG B4189 *********************** 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 357 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 325 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3955 MET cc_start: 0.6290 (ttm) cc_final: 0.6055 (ttm) REVERT: A 3999 MET cc_start: 0.6698 (mmm) cc_final: 0.6457 (mmp) REVERT: A 4043 GLN cc_start: 0.8193 (mm110) cc_final: 0.7636 (mm-40) REVERT: A 4633 GLU cc_start: 0.6794 (tp30) cc_final: 0.6306 (pp20) REVERT: A 4684 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: A 4911 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7534 (mm) REVERT: A 4980 LEU cc_start: 0.8349 (mt) cc_final: 0.7859 (tp) REVERT: A 5027 CYS cc_start: 0.8097 (p) cc_final: 0.7818 (p) REVERT: B 3955 MET cc_start: 0.6280 (ttm) cc_final: 0.6042 (ttm) REVERT: B 3999 MET cc_start: 0.6711 (mmm) cc_final: 0.6470 (mmp) REVERT: B 4043 GLN cc_start: 0.8192 (mm110) cc_final: 0.7639 (mm-40) REVERT: B 4633 GLU cc_start: 0.6776 (tp30) cc_final: 0.6338 (pp20) REVERT: B 4684 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: B 4911 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7528 (mm) REVERT: B 4980 LEU cc_start: 0.8347 (mt) cc_final: 0.7853 (tp) REVERT: B 5027 CYS cc_start: 0.8097 (p) cc_final: 0.7816 (p) REVERT: C 3955 MET cc_start: 0.6289 (ttm) cc_final: 0.6053 (ttm) REVERT: C 3999 MET cc_start: 0.6706 (mmm) cc_final: 0.6465 (mmp) REVERT: C 4043 GLN cc_start: 0.8189 (mm110) cc_final: 0.7633 (mm-40) REVERT: C 4633 GLU cc_start: 0.6765 (tp30) cc_final: 0.6327 (pp20) REVERT: C 4684 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: C 4911 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7525 (mm) REVERT: C 4980 LEU cc_start: 0.8357 (mt) cc_final: 0.7869 (tp) REVERT: C 5027 CYS cc_start: 0.8102 (p) cc_final: 0.7826 (p) REVERT: D 3955 MET cc_start: 0.6295 (ttm) cc_final: 0.6057 (ttm) REVERT: D 3999 MET cc_start: 0.6697 (mmm) cc_final: 0.6454 (mmp) REVERT: D 4043 GLN cc_start: 0.8195 (mm110) cc_final: 0.7633 (mm-40) REVERT: D 4633 GLU cc_start: 0.6782 (tp30) cc_final: 0.6324 (pp20) REVERT: D 4684 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: D 4911 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7519 (mm) REVERT: D 4980 LEU cc_start: 0.8346 (mt) cc_final: 0.7860 (tp) REVERT: D 5027 CYS cc_start: 0.8097 (p) cc_final: 0.7819 (p) outliers start: 32 outliers final: 8 residues processed: 345 average time/residue: 1.4762 time to fit residues: 567.7510 Evaluate side-chains 331 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 315 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3987 ASP Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain B residue 3987 ASP Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain C residue 3987 ASP Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain D residue 3987 ASP Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4911 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 151 optimal weight: 0.1980 chunk 226 optimal weight: 0.5980 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4223 ASN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21160 Z= 0.150 Angle : 0.457 7.012 28576 Z= 0.242 Chirality : 0.034 0.118 3092 Planarity : 0.003 0.036 3604 Dihedral : 12.124 163.351 2748 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.65 % Allowed : 10.94 % Favored : 87.41 % 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: 2.15 (0.17), residues: 2472 helix: 2.21 (0.12), residues: 1644 sheet: 0.20 (0.50), residues: 104 loop : -0.20 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D4644 HIS 0.004 0.001 HIS B3998 PHE 0.012 0.001 PHE A4219 TYR 0.009 0.001 TYR C4994 ARG 0.008 0.000 ARG A4189 *********************** 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 352 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 315 time to evaluate : 2.608 Fit side-chains REVERT: A 3999 MET cc_start: 0.6709 (mmm) cc_final: 0.6468 (mmp) REVERT: A 4043 GLN cc_start: 0.8164 (mm110) cc_final: 0.7581 (mm110) REVERT: A 4212 GLU cc_start: 0.7935 (tp30) cc_final: 0.7645 (tp30) REVERT: A 4224 GLU cc_start: 0.6726 (pm20) cc_final: 0.6426 (pm20) REVERT: A 4633 GLU cc_start: 0.6797 (tp30) cc_final: 0.6329 (pp20) REVERT: A 4684 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: A 4911 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7552 (mm) REVERT: A 4980 LEU cc_start: 0.8321 (mt) cc_final: 0.7856 (tp) REVERT: B 3999 MET cc_start: 0.6718 (mmm) cc_final: 0.6475 (mmp) REVERT: B 4043 GLN cc_start: 0.8165 (mm110) cc_final: 0.7583 (mm110) REVERT: B 4212 GLU cc_start: 0.7944 (tp30) cc_final: 0.7654 (tp30) REVERT: B 4224 GLU cc_start: 0.6728 (pm20) cc_final: 0.6428 (pm20) REVERT: B 4633 GLU cc_start: 0.6777 (tp30) cc_final: 0.6358 (pp20) REVERT: B 4684 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: B 4911 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7546 (mm) REVERT: B 4980 LEU cc_start: 0.8321 (mt) cc_final: 0.7852 (tp) REVERT: C 3999 MET cc_start: 0.6710 (mmm) cc_final: 0.6468 (mmp) REVERT: C 4043 GLN cc_start: 0.8162 (mm110) cc_final: 0.7583 (mm110) REVERT: C 4212 GLU cc_start: 0.7934 (tp30) cc_final: 0.7646 (tp30) REVERT: C 4224 GLU cc_start: 0.6713 (pm20) cc_final: 0.6409 (pm20) REVERT: C 4633 GLU cc_start: 0.6761 (tp30) cc_final: 0.6346 (pp20) REVERT: C 4684 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: C 4851 TYR cc_start: 0.8662 (m-80) cc_final: 0.8436 (m-80) REVERT: C 4911 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7545 (mm) REVERT: C 4980 LEU cc_start: 0.8324 (mt) cc_final: 0.7862 (tp) REVERT: D 3999 MET cc_start: 0.6704 (mmm) cc_final: 0.6463 (mmp) REVERT: D 4043 GLN cc_start: 0.8165 (mm110) cc_final: 0.7579 (mm110) REVERT: D 4212 GLU cc_start: 0.7928 (tp30) cc_final: 0.7639 (tp30) REVERT: D 4224 GLU cc_start: 0.6707 (pm20) cc_final: 0.6405 (pm20) REVERT: D 4633 GLU cc_start: 0.6783 (tp30) cc_final: 0.6344 (pp20) REVERT: D 4684 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: D 4911 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7538 (mm) REVERT: D 4980 LEU cc_start: 0.8319 (mt) cc_final: 0.7859 (tp) outliers start: 37 outliers final: 8 residues processed: 328 average time/residue: 1.4963 time to fit residues: 546.7414 Evaluate side-chains 334 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 318 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 GLN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4933 GLN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 GLN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21160 Z= 0.211 Angle : 0.489 8.360 28576 Z= 0.256 Chirality : 0.035 0.124 3092 Planarity : 0.003 0.041 3604 Dihedral : 12.167 163.092 2748 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.23 % Allowed : 10.85 % 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: 2.07 (0.17), residues: 2472 helix: 2.15 (0.12), residues: 1644 sheet: 0.05 (0.50), residues: 104 loop : -0.23 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A4716 HIS 0.004 0.001 HIS A3998 PHE 0.013 0.001 PHE B4916 TYR 0.011 0.001 TYR B4994 ARG 0.009 0.001 ARG A4189 *********************** 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 372 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 322 time to evaluate : 2.569 Fit side-chains REVERT: A 3955 MET cc_start: 0.6324 (ttm) cc_final: 0.6058 (ttm) REVERT: A 3987 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: A 3999 MET cc_start: 0.6709 (mmm) cc_final: 0.6471 (mmp) REVERT: A 4043 GLN cc_start: 0.8185 (mm110) cc_final: 0.7602 (mm110) REVERT: A 4204 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6863 (mt0) REVERT: A 4212 GLU cc_start: 0.7946 (tp30) cc_final: 0.7635 (tp30) REVERT: A 4633 GLU cc_start: 0.6853 (tp30) cc_final: 0.6322 (pp20) REVERT: A 4684 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: A 4796 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7667 (tmm) REVERT: A 4880 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7970 (tpp) REVERT: A 4911 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7550 (mm) REVERT: A 4980 LEU cc_start: 0.8328 (mt) cc_final: 0.7873 (tp) REVERT: A 5027 CYS cc_start: 0.8112 (p) cc_final: 0.7841 (p) REVERT: B 3955 MET cc_start: 0.6318 (ttm) cc_final: 0.6051 (ttm) REVERT: B 3999 MET cc_start: 0.6724 (mmm) cc_final: 0.6481 (mmp) REVERT: B 4043 GLN cc_start: 0.8184 (mm110) cc_final: 0.7607 (mm110) REVERT: B 4204 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6857 (mt0) REVERT: B 4212 GLU cc_start: 0.7952 (tp30) cc_final: 0.7640 (tp30) REVERT: B 4633 GLU cc_start: 0.6836 (tp30) cc_final: 0.6355 (pp20) REVERT: B 4684 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: B 4796 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7683 (tmm) REVERT: B 4880 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7991 (tpp) REVERT: B 4911 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7549 (mm) REVERT: B 4980 LEU cc_start: 0.8327 (mt) cc_final: 0.7861 (tp) REVERT: B 5027 CYS cc_start: 0.8108 (p) cc_final: 0.7838 (p) REVERT: C 3955 MET cc_start: 0.6328 (ttm) cc_final: 0.6062 (ttm) REVERT: C 3999 MET cc_start: 0.6713 (mmm) cc_final: 0.6472 (mmp) REVERT: C 4043 GLN cc_start: 0.8181 (mm110) cc_final: 0.7604 (mm110) REVERT: C 4204 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6858 (mt0) REVERT: C 4212 GLU cc_start: 0.7946 (tp30) cc_final: 0.7634 (tp30) REVERT: C 4633 GLU cc_start: 0.6823 (tp30) cc_final: 0.6346 (pp20) REVERT: C 4684 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: C 4796 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7684 (tmm) REVERT: C 4911 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7551 (mm) REVERT: C 4980 LEU cc_start: 0.8334 (mt) cc_final: 0.7883 (tp) REVERT: C 5027 CYS cc_start: 0.8112 (p) cc_final: 0.7848 (p) REVERT: D 3955 MET cc_start: 0.6329 (ttm) cc_final: 0.6063 (ttm) REVERT: D 3987 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: D 3999 MET cc_start: 0.6706 (mmm) cc_final: 0.6466 (mmp) REVERT: D 4043 GLN cc_start: 0.8184 (mm110) cc_final: 0.7600 (mm110) REVERT: D 4204 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6868 (mt0) REVERT: D 4212 GLU cc_start: 0.7940 (tp30) cc_final: 0.7628 (tp30) REVERT: D 4633 GLU cc_start: 0.6840 (tp30) cc_final: 0.6340 (pp20) REVERT: D 4684 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: D 4796 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7681 (tmm) REVERT: D 4911 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7539 (mm) REVERT: D 4980 LEU cc_start: 0.8325 (mt) cc_final: 0.7876 (tp) REVERT: D 5027 CYS cc_start: 0.8107 (p) cc_final: 0.7841 (p) outliers start: 50 outliers final: 12 residues processed: 342 average time/residue: 1.4494 time to fit residues: 553.1344 Evaluate side-chains 340 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 308 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3987 ASP Chi-restraints excluded: chain A residue 4000 MET Chi-restraints excluded: chain A residue 4204 GLN Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4204 GLN Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4880 MET Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4204 GLN Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 3987 ASP Chi-restraints excluded: chain D residue 4000 MET Chi-restraints excluded: chain D residue 4204 GLN Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.9990 chunk 215 optimal weight: 0.0070 chunk 47 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 59 optimal weight: 0.0050 chunk 239 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 111 optimal weight: 0.0970 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21160 Z= 0.138 Angle : 0.449 6.599 28576 Z= 0.238 Chirality : 0.033 0.112 3092 Planarity : 0.003 0.043 3604 Dihedral : 12.086 163.215 2748 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.14 % Allowed : 12.68 % Favored : 85.18 % 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: 2.27 (0.17), residues: 2472 helix: 2.29 (0.12), residues: 1668 sheet: 0.26 (0.50), residues: 104 loop : -0.23 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B4644 HIS 0.002 0.001 HIS B3998 PHE 0.013 0.001 PHE A4219 TYR 0.010 0.001 TYR C4687 ARG 0.008 0.000 ARG C4189 *********************** 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 368 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 320 time to evaluate : 2.333 Fit side-chains REVERT: A 3955 MET cc_start: 0.6353 (ttm) cc_final: 0.6100 (ttm) REVERT: A 3987 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6888 (m-30) REVERT: A 4189 ARG cc_start: 0.7916 (ptm160) cc_final: 0.7587 (ptm160) REVERT: A 4204 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: A 4212 GLU cc_start: 0.7897 (tp30) cc_final: 0.7665 (tp30) REVERT: A 4633 GLU cc_start: 0.6827 (tp30) cc_final: 0.6296 (pp20) REVERT: A 4684 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7698 (m-30) REVERT: A 4796 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7616 (tmm) REVERT: A 4821 LYS cc_start: 0.8130 (tmtp) cc_final: 0.7852 (tmtm) REVERT: A 4880 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7959 (tpp) REVERT: A 4911 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7607 (mm) REVERT: A 4980 LEU cc_start: 0.8308 (mt) cc_final: 0.7846 (tp) REVERT: B 3987 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: B 3999 MET cc_start: 0.6699 (mmm) cc_final: 0.6482 (mmp) REVERT: B 4189 ARG cc_start: 0.7913 (ptm160) cc_final: 0.7585 (ptm160) REVERT: B 4204 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6885 (mt0) REVERT: B 4212 GLU cc_start: 0.7908 (tp30) cc_final: 0.7674 (tp30) REVERT: B 4633 GLU cc_start: 0.6809 (tp30) cc_final: 0.6326 (pp20) REVERT: B 4684 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: B 4796 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7627 (tmm) REVERT: B 4821 LYS cc_start: 0.8124 (tmtp) cc_final: 0.7848 (tmtm) REVERT: B 4911 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7607 (mm) REVERT: B 4980 LEU cc_start: 0.8310 (mt) cc_final: 0.7846 (tp) REVERT: C 3987 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6896 (m-30) REVERT: C 3999 MET cc_start: 0.6694 (mmm) cc_final: 0.6480 (mmp) REVERT: C 4189 ARG cc_start: 0.7916 (ptm160) cc_final: 0.7589 (ptm160) REVERT: C 4204 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6887 (mt0) REVERT: C 4212 GLU cc_start: 0.7897 (tp30) cc_final: 0.7665 (tp30) REVERT: C 4633 GLU cc_start: 0.6792 (tp30) cc_final: 0.6320 (pp20) REVERT: C 4684 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: C 4796 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7633 (tmm) REVERT: C 4821 LYS cc_start: 0.8124 (tmtp) cc_final: 0.7845 (tmtm) REVERT: C 4851 TYR cc_start: 0.8643 (m-80) cc_final: 0.8418 (m-80) REVERT: C 4911 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7608 (mm) REVERT: C 4980 LEU cc_start: 0.8312 (mt) cc_final: 0.7853 (tp) REVERT: D 3955 MET cc_start: 0.6354 (ttm) cc_final: 0.6100 (ttm) REVERT: D 3987 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6882 (m-30) REVERT: D 4189 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7576 (ptm160) REVERT: D 4204 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6890 (mt0) REVERT: D 4212 GLU cc_start: 0.7893 (tp30) cc_final: 0.7658 (tp30) REVERT: D 4633 GLU cc_start: 0.6809 (tp30) cc_final: 0.6313 (pp20) REVERT: D 4684 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: D 4796 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7627 (tmm) REVERT: D 4821 LYS cc_start: 0.8125 (tmtp) cc_final: 0.7850 (tmtm) REVERT: D 4911 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7592 (mm) REVERT: D 4980 LEU cc_start: 0.8305 (mt) cc_final: 0.7849 (tp) outliers start: 48 outliers final: 12 residues processed: 334 average time/residue: 1.5538 time to fit residues: 576.9449 Evaluate side-chains 344 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 311 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3987 ASP Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4204 GLN Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 3987 ASP Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4204 GLN Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 3987 ASP Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4204 GLN Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 3987 ASP Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4204 GLN Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 0.0980 chunk 175 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4933 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21160 Z= 0.215 Angle : 0.499 8.257 28576 Z= 0.262 Chirality : 0.035 0.116 3092 Planarity : 0.003 0.038 3604 Dihedral : 12.151 163.014 2748 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.37 % Allowed : 13.35 % Favored : 84.29 % 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: 2.12 (0.17), residues: 2472 helix: 2.19 (0.12), residues: 1668 sheet: 0.02 (0.49), residues: 104 loop : -0.26 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A4644 HIS 0.004 0.001 HIS A3998 PHE 0.014 0.001 PHE C4219 TYR 0.011 0.001 TYR D4994 ARG 0.008 0.001 ARG D4189 *********************** REFINEMENT MACRO_CYCLE 7 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 364 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 311 time to evaluate : 2.473 Fit side-chains REVERT: A 3987 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6906 (m-30) REVERT: A 4039 MET cc_start: 0.6550 (tmt) cc_final: 0.5705 (tmm) REVERT: A 4043 GLN cc_start: 0.8277 (mm110) cc_final: 0.7714 (mm110) REVERT: A 4184 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.6778 (tmm) REVERT: A 4189 ARG cc_start: 0.7933 (ptm160) cc_final: 0.7643 (ptm160) REVERT: A 4204 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6925 (mt0) REVERT: A 4212 GLU cc_start: 0.7918 (tp30) cc_final: 0.7647 (tp30) REVERT: A 4633 GLU cc_start: 0.6867 (tp30) cc_final: 0.6310 (pp20) REVERT: A 4684 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: A 4911 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7560 (mm) REVERT: A 4980 LEU cc_start: 0.8320 (mt) cc_final: 0.7856 (tp) REVERT: A 5027 CYS cc_start: 0.8102 (p) cc_final: 0.7838 (p) REVERT: B 3987 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6921 (m-30) REVERT: B 3999 MET cc_start: 0.6704 (mmm) cc_final: 0.6474 (mmp) REVERT: B 4039 MET cc_start: 0.6539 (tmt) cc_final: 0.5693 (tmm) REVERT: B 4043 GLN cc_start: 0.8281 (mm110) cc_final: 0.7718 (mm110) REVERT: B 4184 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.6765 (tmm) REVERT: B 4189 ARG cc_start: 0.7933 (ptm160) cc_final: 0.7639 (ptm160) REVERT: B 4204 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6869 (mt0) REVERT: B 4212 GLU cc_start: 0.7926 (tp30) cc_final: 0.7655 (tp30) REVERT: B 4633 GLU cc_start: 0.6849 (tp30) cc_final: 0.6286 (pp20) REVERT: B 4684 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: B 4911 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7557 (mm) REVERT: B 4980 LEU cc_start: 0.8320 (mt) cc_final: 0.7857 (tp) REVERT: B 5027 CYS cc_start: 0.8101 (p) cc_final: 0.7835 (p) REVERT: C 3987 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: C 3999 MET cc_start: 0.6694 (mmm) cc_final: 0.6487 (mmp) REVERT: C 4039 MET cc_start: 0.6533 (tmt) cc_final: 0.5688 (tmm) REVERT: C 4043 GLN cc_start: 0.8276 (mm110) cc_final: 0.7718 (mm110) REVERT: C 4184 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.6767 (tmm) REVERT: C 4189 ARG cc_start: 0.7936 (ptm160) cc_final: 0.7643 (ptm160) REVERT: C 4204 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6871 (mt0) REVERT: C 4212 GLU cc_start: 0.7915 (tp30) cc_final: 0.7645 (tp30) REVERT: C 4633 GLU cc_start: 0.6835 (tp30) cc_final: 0.6278 (pp20) REVERT: C 4684 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: C 4911 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7558 (mm) REVERT: C 4922 PHE cc_start: 0.7875 (t80) cc_final: 0.7501 (m-80) REVERT: C 4980 LEU cc_start: 0.8324 (mt) cc_final: 0.7867 (tp) REVERT: C 5027 CYS cc_start: 0.8109 (p) cc_final: 0.7847 (p) REVERT: D 3987 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: D 4039 MET cc_start: 0.6533 (tmt) cc_final: 0.5686 (tmm) REVERT: D 4043 GLN cc_start: 0.8282 (mm110) cc_final: 0.7714 (mm110) REVERT: D 4184 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.6779 (tmm) REVERT: D 4189 ARG cc_start: 0.7931 (ptm160) cc_final: 0.7641 (ptm160) REVERT: D 4204 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6873 (mt0) REVERT: D 4212 GLU cc_start: 0.7911 (tp30) cc_final: 0.7641 (tp30) REVERT: D 4633 GLU cc_start: 0.6852 (tp30) cc_final: 0.6271 (pp20) REVERT: D 4684 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: D 4911 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7545 (mm) REVERT: D 4980 LEU cc_start: 0.8316 (mt) cc_final: 0.7861 (tp) REVERT: D 5027 CYS cc_start: 0.8099 (p) cc_final: 0.7832 (p) outliers start: 53 outliers final: 12 residues processed: 335 average time/residue: 1.4994 time to fit residues: 559.8005 Evaluate side-chains 341 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 309 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3987 ASP Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4204 GLN Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 3987 ASP Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4204 GLN Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 3987 ASP Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4204 GLN Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 3987 ASP Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4204 GLN Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4933 GLN B4997 ASN D4933 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21160 Z= 0.206 Angle : 0.484 7.449 28576 Z= 0.257 Chirality : 0.035 0.116 3092 Planarity : 0.003 0.031 3604 Dihedral : 12.138 163.049 2748 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.65 % Allowed : 14.42 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.17), residues: 2472 helix: 2.15 (0.12), residues: 1668 sheet: 0.10 (0.50), residues: 104 loop : -0.23 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A4716 HIS 0.003 0.001 HIS B3998 PHE 0.012 0.001 PHE C4916 TYR 0.011 0.001 TYR C4994 ARG 0.007 0.001 ARG A4189 *********************** REFINEMENT MACRO_CYCLE 8 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 355 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 318 time to evaluate : 2.539 Fit side-chains REVERT: A 3955 MET cc_start: 0.6201 (ttm) cc_final: 0.5947 (ttm) REVERT: A 3987 ASP cc_start: 0.7230 (m-30) cc_final: 0.6908 (m-30) REVERT: A 4039 MET cc_start: 0.6566 (tmt) cc_final: 0.5646 (tmm) REVERT: A 4043 GLN cc_start: 0.8270 (mm110) cc_final: 0.7754 (mm110) REVERT: A 4204 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6908 (mt0) REVERT: A 4212 GLU cc_start: 0.7925 (tp30) cc_final: 0.7662 (tp30) REVERT: A 4633 GLU cc_start: 0.6875 (tp30) cc_final: 0.6254 (pp20) REVERT: A 4684 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: A 4821 LYS cc_start: 0.8136 (tmtp) cc_final: 0.7872 (tmtm) REVERT: A 4911 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7474 (mm) REVERT: A 4922 PHE cc_start: 0.7926 (t80) cc_final: 0.7587 (m-80) REVERT: A 4980 LEU cc_start: 0.8324 (mt) cc_final: 0.7859 (tp) REVERT: A 5027 CYS cc_start: 0.8101 (p) cc_final: 0.7833 (p) REVERT: B 3987 ASP cc_start: 0.7221 (m-30) cc_final: 0.6928 (m-30) REVERT: B 3999 MET cc_start: 0.6539 (mmm) cc_final: 0.6313 (mmp) REVERT: B 4039 MET cc_start: 0.6556 (tmt) cc_final: 0.5631 (tmm) REVERT: B 4043 GLN cc_start: 0.8273 (mm110) cc_final: 0.7759 (mm110) REVERT: B 4204 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6841 (mt0) REVERT: B 4212 GLU cc_start: 0.7934 (tp30) cc_final: 0.7674 (tp30) REVERT: B 4633 GLU cc_start: 0.6856 (tp30) cc_final: 0.6285 (pp20) REVERT: B 4684 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: B 4821 LYS cc_start: 0.8133 (tmtp) cc_final: 0.7865 (tmtm) REVERT: B 4911 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7450 (mm) REVERT: B 4922 PHE cc_start: 0.7881 (t80) cc_final: 0.7503 (m-80) REVERT: B 4980 LEU cc_start: 0.8320 (mt) cc_final: 0.7856 (tp) REVERT: B 5027 CYS cc_start: 0.8100 (p) cc_final: 0.7832 (p) REVERT: C 3987 ASP cc_start: 0.7216 (m-30) cc_final: 0.6923 (m-30) REVERT: C 3999 MET cc_start: 0.6554 (mmm) cc_final: 0.6335 (mmp) REVERT: C 4039 MET cc_start: 0.6548 (tmt) cc_final: 0.5629 (tmm) REVERT: C 4043 GLN cc_start: 0.8269 (mm110) cc_final: 0.7759 (mm110) REVERT: C 4204 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6844 (mt0) REVERT: C 4212 GLU cc_start: 0.7924 (tp30) cc_final: 0.7667 (tp30) REVERT: C 4633 GLU cc_start: 0.6842 (tp30) cc_final: 0.6272 (pp20) REVERT: C 4684 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: C 4821 LYS cc_start: 0.8132 (tmtp) cc_final: 0.7864 (tmtm) REVERT: C 4911 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7476 (mm) REVERT: C 4980 LEU cc_start: 0.8327 (mt) cc_final: 0.7865 (tp) REVERT: C 5027 CYS cc_start: 0.8110 (p) cc_final: 0.7843 (p) REVERT: D 3955 MET cc_start: 0.6197 (ttm) cc_final: 0.5946 (ttm) REVERT: D 3987 ASP cc_start: 0.7225 (m-30) cc_final: 0.6907 (m-30) REVERT: D 4039 MET cc_start: 0.6550 (tmt) cc_final: 0.5626 (tmm) REVERT: D 4043 GLN cc_start: 0.8278 (mm110) cc_final: 0.7756 (mm110) REVERT: D 4204 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6851 (mt0) REVERT: D 4212 GLU cc_start: 0.7920 (tp30) cc_final: 0.7659 (tp30) REVERT: D 4633 GLU cc_start: 0.6859 (tp30) cc_final: 0.6270 (pp20) REVERT: D 4684 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7698 (m-30) REVERT: D 4821 LYS cc_start: 0.8133 (tmtp) cc_final: 0.7871 (tmtm) REVERT: D 4911 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7444 (mm) REVERT: D 4922 PHE cc_start: 0.7897 (t80) cc_final: 0.7551 (m-80) REVERT: D 4980 LEU cc_start: 0.8318 (mt) cc_final: 0.7858 (tp) REVERT: D 5027 CYS cc_start: 0.8100 (p) cc_final: 0.7831 (p) outliers start: 37 outliers final: 12 residues processed: 328 average time/residue: 1.5398 time to fit residues: 560.8710 Evaluate side-chains 339 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 315 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4204 GLN Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4204 GLN Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4204 GLN Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4204 GLN Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4933 GLN B4933 GLN B4997 ASN D4933 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21160 Z= 0.237 Angle : 0.536 10.984 28576 Z= 0.278 Chirality : 0.036 0.123 3092 Planarity : 0.003 0.033 3604 Dihedral : 12.162 162.875 2748 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.88 % Allowed : 14.15 % Favored : 83.97 % 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: 2.03 (0.17), residues: 2472 helix: 2.09 (0.12), residues: 1664 sheet: 0.05 (0.50), residues: 104 loop : -0.22 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B4716 HIS 0.004 0.001 HIS A3998 PHE 0.018 0.001 PHE A4219 TYR 0.017 0.001 TYR A4177 ARG 0.007 0.000 ARG C4189 *********************** REFINEMENT MACRO_CYCLE 9 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 362 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 320 time to evaluate : 2.180 Fit side-chains REVERT: A 3987 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: A 4039 MET cc_start: 0.6590 (tmt) cc_final: 0.5783 (tmm) REVERT: A 4043 GLN cc_start: 0.8315 (mm110) cc_final: 0.7818 (mm110) REVERT: A 4184 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.6412 (tmm) REVERT: A 4204 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6838 (mt0) REVERT: A 4212 GLU cc_start: 0.7935 (tp30) cc_final: 0.7654 (tp30) REVERT: A 4633 GLU cc_start: 0.6949 (tp30) cc_final: 0.6251 (pp20) REVERT: A 4684 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: A 4821 LYS cc_start: 0.8160 (tmtp) cc_final: 0.7888 (tmtm) REVERT: A 4911 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7461 (mm) REVERT: A 4922 PHE cc_start: 0.7928 (t80) cc_final: 0.7587 (m-80) REVERT: A 4980 LEU cc_start: 0.8328 (mt) cc_final: 0.7869 (tp) REVERT: A 5027 CYS cc_start: 0.8092 (p) cc_final: 0.7824 (p) REVERT: B 3987 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6787 (m-30) REVERT: B 3999 MET cc_start: 0.6327 (mmm) cc_final: 0.6074 (mmp) REVERT: B 4039 MET cc_start: 0.6573 (tmt) cc_final: 0.5767 (tmm) REVERT: B 4043 GLN cc_start: 0.8318 (mm110) cc_final: 0.7823 (mm110) REVERT: B 4184 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.6407 (tmm) REVERT: B 4204 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6861 (mt0) REVERT: B 4212 GLU cc_start: 0.7945 (tp30) cc_final: 0.7666 (tp30) REVERT: B 4633 GLU cc_start: 0.6934 (tp30) cc_final: 0.6288 (pp20) REVERT: B 4684 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: B 4821 LYS cc_start: 0.8154 (tmtp) cc_final: 0.7881 (tmtm) REVERT: B 4911 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7461 (mm) REVERT: B 4922 PHE cc_start: 0.7890 (t80) cc_final: 0.7504 (m-80) REVERT: B 4980 LEU cc_start: 0.8325 (mt) cc_final: 0.7866 (tp) REVERT: B 5027 CYS cc_start: 0.8091 (p) cc_final: 0.7827 (p) REVERT: C 3987 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6781 (m-30) REVERT: C 3999 MET cc_start: 0.6326 (mmm) cc_final: 0.6079 (mmp) REVERT: C 4039 MET cc_start: 0.6570 (tmt) cc_final: 0.5765 (tmm) REVERT: C 4043 GLN cc_start: 0.8315 (mm110) cc_final: 0.7823 (mm110) REVERT: C 4184 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.6407 (tmm) REVERT: C 4204 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6865 (mt0) REVERT: C 4212 GLU cc_start: 0.7936 (tp30) cc_final: 0.7658 (tp30) REVERT: C 4633 GLU cc_start: 0.6921 (tp30) cc_final: 0.6277 (pp20) REVERT: C 4684 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: C 4821 LYS cc_start: 0.8154 (tmtp) cc_final: 0.7880 (tmtm) REVERT: C 4911 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7464 (mm) REVERT: C 4980 LEU cc_start: 0.8332 (mt) cc_final: 0.7876 (tp) REVERT: C 5027 CYS cc_start: 0.8094 (p) cc_final: 0.7832 (p) REVERT: D 3987 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: D 4039 MET cc_start: 0.6571 (tmt) cc_final: 0.5759 (tmm) REVERT: D 4043 GLN cc_start: 0.8323 (mm110) cc_final: 0.7820 (mm110) REVERT: D 4184 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.6417 (tmm) REVERT: D 4204 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6868 (mt0) REVERT: D 4212 GLU cc_start: 0.7931 (tp30) cc_final: 0.7651 (tp30) REVERT: D 4633 GLU cc_start: 0.6938 (tp30) cc_final: 0.6275 (pp20) REVERT: D 4684 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: D 4821 LYS cc_start: 0.8155 (tmtp) cc_final: 0.7886 (tmtm) REVERT: D 4911 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7456 (mm) REVERT: D 4922 PHE cc_start: 0.7909 (t80) cc_final: 0.7556 (m-80) REVERT: D 4980 LEU cc_start: 0.8324 (mt) cc_final: 0.7867 (tp) REVERT: D 5027 CYS cc_start: 0.8093 (p) cc_final: 0.7827 (p) outliers start: 42 outliers final: 12 residues processed: 335 average time/residue: 1.4809 time to fit residues: 552.1786 Evaluate side-chains 338 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 306 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3987 ASP Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4204 GLN Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 3987 ASP Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4204 GLN Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 3987 ASP Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4204 GLN Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 3987 ASP Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4204 GLN Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.0970 chunk 143 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 247 optimal weight: 0.5980 chunk 227 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 GLN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4933 GLN B4997 ASN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 GLN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21160 Z= 0.176 Angle : 0.486 8.022 28576 Z= 0.257 Chirality : 0.034 0.112 3092 Planarity : 0.004 0.057 3604 Dihedral : 12.105 163.084 2748 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.70 % Allowed : 14.64 % Favored : 83.66 % 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: 2.12 (0.17), residues: 2472 helix: 2.16 (0.12), residues: 1664 sheet: 0.28 (0.51), residues: 104 loop : -0.22 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B4716 HIS 0.003 0.001 HIS D3998 PHE 0.011 0.001 PHE C4916 TYR 0.014 0.001 TYR C4177 ARG 0.014 0.001 ARG A4189 ********************** REFINEMENT MACRO_CYCLE 10 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 348 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 310 time to evaluate : 2.219 Fit side-chains REVERT: A 3987 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: A 4039 MET cc_start: 0.6558 (tmt) cc_final: 0.5731 (tmm) REVERT: A 4043 GLN cc_start: 0.8280 (mm110) cc_final: 0.7775 (mm110) REVERT: A 4204 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6906 (mt0) REVERT: A 4212 GLU cc_start: 0.7914 (tp30) cc_final: 0.7665 (tp30) REVERT: A 4633 GLU cc_start: 0.6881 (tp30) cc_final: 0.6239 (pp20) REVERT: A 4684 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: A 4821 LYS cc_start: 0.8144 (tmtp) cc_final: 0.7874 (tmtm) REVERT: A 4911 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7430 (mm) REVERT: A 4922 PHE cc_start: 0.7909 (t80) cc_final: 0.7573 (m-80) REVERT: A 4980 LEU cc_start: 0.8321 (mt) cc_final: 0.7863 (tp) REVERT: A 5027 CYS cc_start: 0.8077 (p) cc_final: 0.7813 (p) REVERT: B 3987 ASP cc_start: 0.7189 (m-30) cc_final: 0.6888 (m-30) REVERT: B 3999 MET cc_start: 0.6327 (mmm) cc_final: 0.6105 (mmp) REVERT: B 4039 MET cc_start: 0.6543 (tmt) cc_final: 0.5719 (tmm) REVERT: B 4043 GLN cc_start: 0.8283 (mm110) cc_final: 0.7779 (mm110) REVERT: B 4204 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6826 (mt0) REVERT: B 4212 GLU cc_start: 0.7925 (tp30) cc_final: 0.7678 (tp30) REVERT: B 4633 GLU cc_start: 0.6924 (tp30) cc_final: 0.6286 (pp20) REVERT: B 4684 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: B 4821 LYS cc_start: 0.8138 (tmtp) cc_final: 0.7868 (tmtm) REVERT: B 4911 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7429 (mm) REVERT: B 4922 PHE cc_start: 0.7869 (t80) cc_final: 0.7485 (m-80) REVERT: B 4980 LEU cc_start: 0.8319 (mt) cc_final: 0.7861 (tp) REVERT: B 5027 CYS cc_start: 0.8079 (p) cc_final: 0.7813 (p) REVERT: C 3987 ASP cc_start: 0.7185 (m-30) cc_final: 0.6883 (m-30) REVERT: C 3999 MET cc_start: 0.6325 (mmm) cc_final: 0.6108 (mmp) REVERT: C 4039 MET cc_start: 0.6535 (tmt) cc_final: 0.5717 (tmm) REVERT: C 4043 GLN cc_start: 0.8278 (mm110) cc_final: 0.7778 (mm110) REVERT: C 4204 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6828 (mt0) REVERT: C 4212 GLU cc_start: 0.7915 (tp30) cc_final: 0.7670 (tp30) REVERT: C 4633 GLU cc_start: 0.6907 (tp30) cc_final: 0.6272 (pp20) REVERT: C 4684 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: C 4821 LYS cc_start: 0.8140 (tmtp) cc_final: 0.7868 (tmtm) REVERT: C 4911 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7436 (mm) REVERT: C 4980 LEU cc_start: 0.8324 (mt) cc_final: 0.7869 (tp) REVERT: C 5027 CYS cc_start: 0.8078 (p) cc_final: 0.7823 (p) REVERT: D 3987 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6897 (m-30) REVERT: D 4039 MET cc_start: 0.6536 (tmt) cc_final: 0.5708 (tmm) REVERT: D 4043 GLN cc_start: 0.8285 (mm110) cc_final: 0.7777 (mm110) REVERT: D 4204 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6829 (mt0) REVERT: D 4212 GLU cc_start: 0.7913 (tp30) cc_final: 0.7664 (tp30) REVERT: D 4633 GLU cc_start: 0.6923 (tp30) cc_final: 0.6268 (pp20) REVERT: D 4684 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: D 4821 LYS cc_start: 0.8141 (tmtp) cc_final: 0.7874 (tmtm) REVERT: D 4911 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7431 (mm) REVERT: D 4922 PHE cc_start: 0.7887 (t80) cc_final: 0.7533 (m-80) REVERT: D 4980 LEU cc_start: 0.8315 (mt) cc_final: 0.7859 (tp) REVERT: D 5027 CYS cc_start: 0.8079 (p) cc_final: 0.7814 (p) outliers start: 38 outliers final: 15 residues processed: 321 average time/residue: 1.5542 time to fit residues: 554.1605 Evaluate side-chains 334 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 305 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3987 ASP Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4204 GLN Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4204 GLN Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4204 GLN Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 3987 ASP Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4204 GLN Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 GLN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4933 GLN B4997 ASN D4933 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.189951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130459 restraints weight = 23210.066| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.68 r_work: 0.3280 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21160 Z= 0.174 Angle : 0.526 13.348 28576 Z= 0.270 Chirality : 0.034 0.112 3092 Planarity : 0.004 0.058 3604 Dihedral : 12.096 163.081 2748 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.61 % Allowed : 14.69 % Favored : 83.71 % 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: 2472 helix: 2.19 (0.12), residues: 1664 sheet: 0.34 (0.51), residues: 104 loop : -0.24 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A4716 HIS 0.003 0.001 HIS B3998 PHE 0.019 0.001 PHE C4219 TYR 0.010 0.001 TYR C4994 ARG 0.013 0.001 ARG C4189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8736.71 seconds wall clock time: 154 minutes 40.73 seconds (9280.73 seconds total)