Starting phenix.real_space_refine on Sat Mar 16 21:59:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drp_27680/03_2024/8drp_27680_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drp_27680/03_2024/8drp_27680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drp_27680/03_2024/8drp_27680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drp_27680/03_2024/8drp_27680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drp_27680/03_2024/8drp_27680_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drp_27680/03_2024/8drp_27680_updated.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 12 5.49 5 S 104 5.16 5 C 10444 2.51 5 N 2564 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4232": "OE1" <-> "OE2" Residue "A GLU 4239": "OE1" <-> "OE2" Residue "A GLU 4948": "OE1" <-> "OE2" Residue "A GLU 4955": "OE1" <-> "OE2" Residue "B GLU 4232": "OE1" <-> "OE2" Residue "B GLU 4239": "OE1" <-> "OE2" Residue "B GLU 4948": "OE1" <-> "OE2" Residue "B GLU 4955": "OE1" <-> "OE2" Residue "C GLU 4232": "OE1" <-> "OE2" Residue "C GLU 4239": "OE1" <-> "OE2" Residue "C GLU 4948": "OE1" <-> "OE2" Residue "C GLU 4955": "OE1" <-> "OE2" Residue "D GLU 4232": "OE1" <-> "OE2" Residue "D GLU 4239": "OE1" <-> "OE2" Residue "D GLU 4948": "OE1" <-> "OE2" Residue "D GLU 4955": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15816 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3908 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 13, 'TRANS': 498} Chain breaks: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 18, 'GLU:plan': 31, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 241 Chain: "B" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3908 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 13, 'TRANS': 498} Chain breaks: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 18, 'GLU:plan': 31, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 241 Chain: "C" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3908 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 13, 'TRANS': 498} Chain breaks: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 18, 'GLU:plan': 31, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 241 Chain: "D" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3908 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 13, 'TRANS': 498} Chain breaks: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 18, 'GLU:plan': 31, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 241 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3304 SG CYS A4958 52.160 71.994 24.915 1.00 58.39 S ATOM 3329 SG CYS A4961 52.612 70.689 21.409 1.00 57.00 S ATOM 7212 SG CYS B4958 73.526 52.160 24.915 1.00 58.39 S ATOM 7237 SG CYS B4961 74.831 52.612 21.409 1.00 57.00 S ATOM 11120 SG CYS C4958 93.359 73.527 24.915 1.00 58.39 S ATOM 11145 SG CYS C4961 92.907 74.832 21.409 1.00 57.00 S ATOM 15028 SG CYS D4958 71.993 93.361 24.915 1.00 58.39 S ATOM 15053 SG CYS D4961 70.688 92.909 21.409 1.00 57.00 S Time building chain proxies: 8.46, per 1000 atoms: 0.53 Number of scatterers: 15816 At special positions: 0 Unit cell: (146.59, 146.59, 109.14, 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 104 16.00 P 12 15.00 O 2688 8.00 N 2564 7.00 C 10444 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=2.01 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.01 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.01 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.01 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: 6.40 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5103 " pdb="ZN ZN A5103 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5103 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5103 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5103 " - pdb=" SG CYS A4958 " pdb=" ZN B5103 " pdb="ZN ZN B5103 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5103 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5103 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5103 " - pdb=" SG CYS B4958 " pdb=" ZN C5103 " pdb="ZN ZN C5103 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5103 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5103 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5103 " - pdb=" SG CYS C4958 " pdb=" ZN D5103 " pdb="ZN ZN D5103 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5103 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5103 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5103 " - pdb=" SG CYS D4958 " Number of angles added : 4 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 8 sheets defined 67.2% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 4199 through 4206 removed outlier: 3.614A pdb=" N TRP A4205 " --> pdb=" O ASN A4201 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU A4206 " --> pdb=" O ARG A4202 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4224 Processing helix chain 'A' and resid 4230 through 4251 Processing helix chain 'A' and resid 4324 through 4340 Processing helix chain 'A' and resid 4542 through 4557 Processing helix chain 'A' and resid 4560 through 4579 removed outlier: 4.319A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4639 through 4664 Processing helix chain 'A' and resid 4666 through 4683 Processing helix chain 'A' and resid 4697 through 4707 removed outlier: 3.706A pdb=" N ARG A4703 " --> pdb=" O GLY A4699 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4767 through 4770 No H-bonds generated for 'chain 'A' and resid 4767 through 4770' Processing helix chain 'A' and resid 4773 through 4784 Processing helix chain 'A' and resid 4787 through 4804 removed outlier: 3.843A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4819 removed outlier: 3.504A pdb=" N ALA A4811 " --> pdb=" O PHE A4808 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.782A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A4831 " --> pdb=" O LEU A4827 " (cutoff:3.500A) Processing helix chain 'A' and resid 4834 through 4858 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 4893 removed outlier: 4.654A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4910 through 4925 Processing helix chain 'A' and resid 4928 through 4956 Processing helix chain 'A' and resid 4965 through 4970 Processing helix chain 'A' and resid 4974 through 4980 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 'B' and resid 4199 through 4206 removed outlier: 3.614A pdb=" N TRP B4205 " --> pdb=" O ASN B4201 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU B4206 " --> pdb=" O ARG B4202 " (cutoff:3.500A) Processing helix chain 'B' and resid 4208 through 4224 Processing helix chain 'B' and resid 4230 through 4251 Processing helix chain 'B' and resid 4324 through 4340 removed outlier: 3.506A pdb=" N VAL B4338 " --> pdb=" O LEU B4334 " (cutoff:3.500A) Processing helix chain 'B' and resid 4542 through 4557 Processing helix chain 'B' and resid 4560 through 4579 removed outlier: 4.319A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4639 through 4664 Processing helix chain 'B' and resid 4666 through 4683 Processing helix chain 'B' and resid 4697 through 4707 removed outlier: 3.706A pdb=" N ARG B4703 " --> pdb=" O GLY B4699 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) Processing helix chain 'B' and resid 4767 through 4770 No H-bonds generated for 'chain 'B' and resid 4767 through 4770' Processing helix chain 'B' and resid 4773 through 4784 Processing helix chain 'B' and resid 4787 through 4804 removed outlier: 3.843A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4819 removed outlier: 3.504A pdb=" N ALA B4811 " --> pdb=" O PHE B4808 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.782A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B4831 " --> pdb=" O LEU B4827 " (cutoff:3.500A) Processing helix chain 'B' and resid 4834 through 4858 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 4893 removed outlier: 4.654A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4910 through 4925 Processing helix chain 'B' and resid 4928 through 4956 Processing helix chain 'B' and resid 4965 through 4970 Processing helix chain 'B' and resid 4974 through 4980 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 'C' and resid 4199 through 4206 removed outlier: 3.614A pdb=" N TRP C4205 " --> pdb=" O ASN C4201 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C4206 " --> pdb=" O ARG C4202 " (cutoff:3.500A) Processing helix chain 'C' and resid 4208 through 4224 Processing helix chain 'C' and resid 4230 through 4251 Processing helix chain 'C' and resid 4324 through 4340 Processing helix chain 'C' and resid 4542 through 4557 Processing helix chain 'C' and resid 4560 through 4579 removed outlier: 4.319A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4639 through 4664 Processing helix chain 'C' and resid 4666 through 4683 Processing helix chain 'C' and resid 4697 through 4707 removed outlier: 3.706A pdb=" N ARG C4703 " --> pdb=" O GLY C4699 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) Processing helix chain 'C' and resid 4767 through 4770 No H-bonds generated for 'chain 'C' and resid 4767 through 4770' Processing helix chain 'C' and resid 4773 through 4784 Processing helix chain 'C' and resid 4787 through 4804 removed outlier: 3.843A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4819 removed outlier: 3.504A pdb=" N ALA C4811 " --> pdb=" O PHE C4808 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.782A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR C4831 " --> pdb=" O LEU C4827 " (cutoff:3.500A) Processing helix chain 'C' and resid 4834 through 4858 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 4893 removed outlier: 4.654A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4910 through 4925 Processing helix chain 'C' and resid 4928 through 4956 Processing helix chain 'C' and resid 4965 through 4970 Processing helix chain 'C' and resid 4974 through 4980 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 'D' and resid 4199 through 4206 removed outlier: 3.614A pdb=" N TRP D4205 " --> pdb=" O ASN D4201 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU D4206 " --> pdb=" O ARG D4202 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4224 Processing helix chain 'D' and resid 4230 through 4251 Processing helix chain 'D' and resid 4324 through 4340 removed outlier: 3.506A pdb=" N VAL D4338 " --> pdb=" O LEU D4334 " (cutoff:3.500A) Processing helix chain 'D' and resid 4542 through 4557 Processing helix chain 'D' and resid 4560 through 4579 removed outlier: 4.319A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4639 through 4664 Processing helix chain 'D' and resid 4666 through 4683 Processing helix chain 'D' and resid 4697 through 4707 removed outlier: 3.706A pdb=" N ARG D4703 " --> pdb=" O GLY D4699 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) Processing helix chain 'D' and resid 4767 through 4770 No H-bonds generated for 'chain 'D' and resid 4767 through 4770' Processing helix chain 'D' and resid 4773 through 4784 Processing helix chain 'D' and resid 4787 through 4804 removed outlier: 3.843A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4819 removed outlier: 3.504A pdb=" N ALA D4811 " --> pdb=" O PHE D4808 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.782A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR D4831 " --> pdb=" O LEU D4827 " (cutoff:3.500A) Processing helix chain 'D' and resid 4834 through 4858 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 4893 removed outlier: 4.654A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4910 through 4925 Processing helix chain 'D' and resid 4928 through 4956 Processing helix chain 'D' and resid 4965 through 4970 Processing helix chain 'D' and resid 4974 through 4980 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 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 978 hydrogen bonds defined for protein. 2802 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: 4.54 Time building geometry restraints manager: 6.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2400 1.32 - 1.44: 4990 1.44 - 1.57: 8678 1.57 - 1.70: 20 1.70 - 1.82: 168 Bond restraints: 16256 Sorted by residual: bond pdb=" C TRP C4336 " pdb=" O TRP C4336 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.17e-02 7.31e+03 1.36e+01 bond pdb=" N ASP C4878 " pdb=" CA ASP C4878 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.90e+00 bond pdb=" N ASP A4878 " pdb=" CA ASP A4878 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.90e+00 bond pdb=" N ASP B4878 " pdb=" CA ASP B4878 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.90e+00 bond pdb=" N ASP D4878 " pdb=" CA ASP D4878 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.90e+00 ... (remaining 16251 not shown) Histogram of bond angle deviations from ideal: 98.77 - 106.98: 411 106.98 - 115.20: 9253 115.20 - 123.41: 12013 123.41 - 131.62: 451 131.62 - 139.84: 52 Bond angle restraints: 22180 Sorted by residual: angle pdb=" N CYS C4882 " pdb=" CA CYS C4882 " pdb=" C CYS C4882 " ideal model delta sigma weight residual 111.82 104.06 7.76 1.16e+00 7.43e-01 4.47e+01 angle pdb=" N CYS B4882 " pdb=" CA CYS B4882 " pdb=" C CYS B4882 " ideal model delta sigma weight residual 111.82 104.06 7.76 1.16e+00 7.43e-01 4.47e+01 angle pdb=" N CYS A4882 " pdb=" CA CYS A4882 " pdb=" C CYS A4882 " ideal model delta sigma weight residual 111.82 104.06 7.76 1.16e+00 7.43e-01 4.47e+01 angle pdb=" N CYS D4882 " pdb=" CA CYS D4882 " pdb=" C CYS D4882 " ideal model delta sigma weight residual 111.82 104.06 7.76 1.16e+00 7.43e-01 4.47e+01 angle pdb=" N PRO D4709 " pdb=" CA PRO D4709 " pdb=" C PRO D4709 " ideal model delta sigma weight residual 114.03 107.72 6.31 1.23e+00 6.61e-01 2.64e+01 ... (remaining 22175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 7864 16.28 - 32.56: 853 32.56 - 48.84: 423 48.84 - 65.11: 80 65.11 - 81.39: 28 Dihedral angle restraints: 9248 sinusoidal: 3244 harmonic: 6004 Sorted by residual: dihedral pdb=" CG ARG A4944 " pdb=" CD ARG A4944 " pdb=" NE ARG A4944 " pdb=" CZ ARG A4944 " ideal model delta sinusoidal sigma weight residual 90.00 131.71 -41.71 2 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CG ARG B4944 " pdb=" CD ARG B4944 " pdb=" NE ARG B4944 " pdb=" CZ ARG B4944 " ideal model delta sinusoidal sigma weight residual 90.00 131.71 -41.71 2 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CG ARG D4944 " pdb=" CD ARG D4944 " pdb=" NE ARG D4944 " pdb=" CZ ARG D4944 " ideal model delta sinusoidal sigma weight residual 90.00 131.71 -41.71 2 1.50e+01 4.44e-03 9.44e+00 ... (remaining 9245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1877 0.040 - 0.081: 454 0.081 - 0.121: 137 0.121 - 0.161: 12 0.161 - 0.202: 8 Chirality restraints: 2488 Sorted by residual: chirality pdb=" CB ILE A4183 " pdb=" CA ILE A4183 " pdb=" CG1 ILE A4183 " pdb=" CG2 ILE A4183 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE C4183 " pdb=" CA ILE C4183 " pdb=" CG1 ILE C4183 " pdb=" CG2 ILE C4183 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE B4183 " pdb=" CA ILE B4183 " pdb=" CG1 ILE B4183 " pdb=" CG2 ILE B4183 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2485 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A4878 " 0.013 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ASP A4878 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP A4878 " 0.018 2.00e-02 2.50e+03 pdb=" N MET A4879 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B4878 " 0.013 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ASP B4878 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP B4878 " 0.018 2.00e-02 2.50e+03 pdb=" N MET B4879 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D4878 " -0.013 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ASP D4878 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP D4878 " -0.018 2.00e-02 2.50e+03 pdb=" N MET D4879 " -0.016 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4497 2.81 - 3.33: 15716 3.33 - 3.85: 27752 3.85 - 4.38: 30137 4.38 - 4.90: 51821 Nonbonded interactions: 129923 Sorted by model distance: nonbonded pdb=" OH TYR B4661 " pdb=" OD2 ASP B4786 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR D4661 " pdb=" OD2 ASP D4786 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR C4661 " pdb=" OD2 ASP C4786 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A4661 " pdb=" OD2 ASP A4786 " model vdw 2.282 2.440 nonbonded pdb=" O CYS C4238 " pdb=" OG1 THR C4241 " model vdw 2.294 2.440 ... (remaining 129918 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: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.050 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 45.700 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16256 Z= 0.274 Angle : 0.706 9.101 22180 Z= 0.442 Chirality : 0.039 0.202 2488 Planarity : 0.004 0.036 2736 Dihedral : 17.638 81.393 5372 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.22 % Allowed : 26.58 % Favored : 70.21 % 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: 1.89 (0.19), residues: 2008 helix: 2.11 (0.13), residues: 1404 sheet: -0.18 (0.52), residues: 104 loop : -0.92 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B4716 HIS 0.001 0.000 HIS B4978 PHE 0.011 0.001 PHE D4711 TYR 0.018 0.001 TYR C5014 ARG 0.007 0.001 ARG A5029 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 292 time to evaluate : 1.801 Fit side-chains REVERT: A 4704 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6048 (tp) REVERT: A 4777 ILE cc_start: 0.7635 (mp) cc_final: 0.7416 (pt) REVERT: A 4778 TRP cc_start: 0.7384 (OUTLIER) cc_final: 0.6135 (t-100) REVERT: B 4704 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6043 (tp) REVERT: B 4777 ILE cc_start: 0.7632 (mp) cc_final: 0.7414 (pt) REVERT: B 4778 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.6133 (t-100) REVERT: C 4704 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6045 (tp) REVERT: C 4777 ILE cc_start: 0.7633 (mp) cc_final: 0.7414 (pt) REVERT: C 4778 TRP cc_start: 0.7380 (OUTLIER) cc_final: 0.6129 (t-100) REVERT: D 4704 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6042 (tp) REVERT: D 4777 ILE cc_start: 0.7639 (mp) cc_final: 0.7420 (pt) REVERT: D 4778 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.6128 (t-100) outliers start: 47 outliers final: 27 residues processed: 335 average time/residue: 1.0096 time to fit residues: 381.3622 Evaluate side-chains 324 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4236 SER Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4778 TRP Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 4236 SER Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 4236 SER Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4338 VAL Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4778 TRP Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 4236 SER Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4662 ASN Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4778 TRP Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4707 ASN A4812 HIS B4707 ASN B4812 HIS C4707 ASN C4812 HIS D4707 ASN D4812 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16256 Z= 0.296 Angle : 0.573 7.205 22180 Z= 0.298 Chirality : 0.039 0.166 2488 Planarity : 0.004 0.036 2736 Dihedral : 10.159 89.321 2399 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.79 % Allowed : 22.74 % Favored : 72.47 % 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: 1.64 (0.18), residues: 2008 helix: 2.01 (0.13), residues: 1400 sheet: -0.61 (0.48), residues: 104 loop : -1.22 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D4716 HIS 0.008 0.002 HIS D5003 PHE 0.017 0.002 PHE A4916 TYR 0.017 0.002 TYR D4994 ARG 0.009 0.001 ARG C4192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 290 time to evaluate : 1.778 Fit side-chains REVERT: A 4879 MET cc_start: 0.8725 (mmm) cc_final: 0.8464 (tpt) REVERT: A 4948 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: B 4879 MET cc_start: 0.8724 (mmm) cc_final: 0.8464 (tpt) REVERT: B 4948 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: C 4879 MET cc_start: 0.8731 (mmm) cc_final: 0.8473 (tpt) REVERT: D 4879 MET cc_start: 0.8726 (mmm) cc_final: 0.8467 (tpt) REVERT: D 4948 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7163 (mp0) outliers start: 70 outliers final: 27 residues processed: 321 average time/residue: 1.0114 time to fit residues: 366.3300 Evaluate side-chains 296 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4558 ASN Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4899 ASP Chi-restraints excluded: chain A residue 4948 GLU Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4558 ASN Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4899 ASP Chi-restraints excluded: chain B residue 4948 GLU Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain C residue 4338 VAL Chi-restraints excluded: chain C residue 4558 ASN Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4899 ASP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4558 ASN Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4899 ASP Chi-restraints excluded: chain D residue 4948 GLU Chi-restraints excluded: chain D residue 4958 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 154 optimal weight: 0.0030 chunk 126 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16256 Z= 0.189 Angle : 0.489 6.637 22180 Z= 0.254 Chirality : 0.035 0.181 2488 Planarity : 0.003 0.037 2736 Dihedral : 9.369 87.821 2359 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.34 % Allowed : 22.74 % Favored : 71.92 % 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: 2.14 (0.19), residues: 2008 helix: 2.31 (0.13), residues: 1360 sheet: -0.76 (0.46), residues: 104 loop : -0.45 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C4716 HIS 0.006 0.001 HIS A5003 PHE 0.011 0.001 PHE C4916 TYR 0.012 0.001 TYR B5009 ARG 0.008 0.001 ARG C4192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 313 time to evaluate : 1.670 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6926 (mtm-85) REVERT: A 4562 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8404 (mm) REVERT: A 4778 TRP cc_start: 0.7389 (OUTLIER) cc_final: 0.5979 (t-100) REVERT: A 4879 MET cc_start: 0.8689 (mmm) cc_final: 0.8466 (tpt) REVERT: A 4948 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: B 4180 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6929 (mtm-85) REVERT: B 4562 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8404 (mm) REVERT: B 4778 TRP cc_start: 0.7385 (OUTLIER) cc_final: 0.5977 (t-100) REVERT: B 4879 MET cc_start: 0.8687 (mmm) cc_final: 0.8468 (tpt) REVERT: B 4948 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: C 4180 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6928 (mtm-85) REVERT: C 4562 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8404 (mm) REVERT: C 4778 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.5971 (t-100) REVERT: C 4879 MET cc_start: 0.8691 (mmm) cc_final: 0.8471 (tpt) REVERT: D 4180 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7031 (mtm-85) REVERT: D 4562 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8408 (mm) REVERT: D 4778 TRP cc_start: 0.7388 (OUTLIER) cc_final: 0.5974 (t-100) REVERT: D 4879 MET cc_start: 0.8692 (mmm) cc_final: 0.8471 (tpt) REVERT: D 4948 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7179 (mp0) outliers start: 78 outliers final: 26 residues processed: 367 average time/residue: 1.0585 time to fit residues: 435.2729 Evaluate side-chains 323 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 282 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4236 SER Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4778 TRP Chi-restraints excluded: chain A residue 4948 GLU Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4236 SER Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain B residue 4948 GLU Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4236 SER Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4778 TRP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4236 SER Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4778 TRP Chi-restraints excluded: chain D residue 4948 GLU Chi-restraints excluded: chain D residue 4958 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 197 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4250 GLN B4250 GLN C4250 GLN D4250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16256 Z= 0.251 Angle : 0.524 5.979 22180 Z= 0.272 Chirality : 0.037 0.199 2488 Planarity : 0.004 0.039 2736 Dihedral : 9.295 89.874 2358 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.45 % Allowed : 25.62 % Favored : 69.93 % 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: 1.93 (0.19), residues: 2008 helix: 2.16 (0.13), residues: 1360 sheet: -0.80 (0.49), residues: 104 loop : -0.56 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A4716 HIS 0.009 0.002 HIS C5003 PHE 0.013 0.001 PHE C4916 TYR 0.014 0.001 TYR D4994 ARG 0.007 0.001 ARG A4192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 288 time to evaluate : 1.926 Fit side-chains REVERT: A 4674 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: A 4778 TRP cc_start: 0.7404 (OUTLIER) cc_final: 0.5979 (t-100) REVERT: A 4879 MET cc_start: 0.8642 (mmm) cc_final: 0.8316 (tpt) REVERT: A 4948 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 4674 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: B 4778 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.5979 (t-100) REVERT: B 4879 MET cc_start: 0.8639 (mmm) cc_final: 0.8318 (tpt) REVERT: B 4948 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: C 4674 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: C 4778 TRP cc_start: 0.7403 (OUTLIER) cc_final: 0.5979 (t-100) REVERT: C 4879 MET cc_start: 0.8642 (mmm) cc_final: 0.8320 (tpt) REVERT: D 4674 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: D 4778 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.5979 (t-100) REVERT: D 4879 MET cc_start: 0.8641 (mmm) cc_final: 0.8319 (tpt) REVERT: D 4948 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7190 (mp0) outliers start: 65 outliers final: 26 residues processed: 330 average time/residue: 1.0599 time to fit residues: 391.0045 Evaluate side-chains 319 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 282 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4236 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4674 GLU Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4778 TRP Chi-restraints excluded: chain A residue 4948 GLU Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain B residue 4236 SER Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4674 GLU Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain B residue 4948 GLU Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain C residue 4236 SER Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4674 GLU Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4778 TRP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain D residue 4236 SER Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4674 GLU Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4778 TRP Chi-restraints excluded: chain D residue 4948 GLU Chi-restraints excluded: chain D residue 4958 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4250 GLN B4250 GLN C4250 GLN D4250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16256 Z= 0.283 Angle : 0.553 7.586 22180 Z= 0.285 Chirality : 0.037 0.224 2488 Planarity : 0.004 0.043 2736 Dihedral : 9.159 85.149 2356 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.27 % Allowed : 25.89 % Favored : 68.84 % 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: 1.74 (0.19), residues: 2008 helix: 1.99 (0.13), residues: 1364 sheet: -0.73 (0.50), residues: 104 loop : -0.61 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A4716 HIS 0.007 0.001 HIS C5003 PHE 0.013 0.002 PHE B4916 TYR 0.015 0.002 TYR A4994 ARG 0.011 0.001 ARG D4192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 282 time to evaluate : 1.657 Fit side-chains REVERT: A 4232 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6203 (tm-30) REVERT: A 4674 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: A 4704 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6360 (pt) REVERT: A 4879 MET cc_start: 0.8626 (mmm) cc_final: 0.8355 (tpt) REVERT: B 4232 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6203 (tm-30) REVERT: B 4674 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: B 4704 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6363 (pt) REVERT: B 4879 MET cc_start: 0.8627 (mmm) cc_final: 0.8357 (tpt) REVERT: C 4232 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6198 (tm-30) REVERT: C 4674 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: C 4879 MET cc_start: 0.8630 (mmm) cc_final: 0.8362 (tpt) REVERT: D 4232 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6197 (tm-30) REVERT: D 4674 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: D 4879 MET cc_start: 0.8628 (mmm) cc_final: 0.8358 (tpt) REVERT: D 4948 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7216 (mp0) outliers start: 77 outliers final: 44 residues processed: 336 average time/residue: 1.0625 time to fit residues: 401.0922 Evaluate side-chains 310 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 259 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4236 SER Chi-restraints excluded: chain A residue 4558 ASN Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4674 GLU Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4236 SER Chi-restraints excluded: chain B residue 4325 ARG Chi-restraints excluded: chain B residue 4558 ASN Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4674 GLU Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4236 SER Chi-restraints excluded: chain C residue 4558 ASN Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4674 GLU Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4236 SER Chi-restraints excluded: chain D residue 4325 ARG Chi-restraints excluded: chain D residue 4558 ASN Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4674 GLU Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4948 GLU Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 38 optimal weight: 0.0970 chunk 115 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 197 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4250 GLN B4250 GLN C4250 GLN D4250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16256 Z= 0.176 Angle : 0.515 7.206 22180 Z= 0.265 Chirality : 0.036 0.226 2488 Planarity : 0.003 0.040 2736 Dihedral : 9.032 81.054 2356 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.45 % Allowed : 27.40 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 2008 helix: 2.11 (0.13), residues: 1364 sheet: -0.69 (0.48), residues: 104 loop : -0.60 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D4716 HIS 0.005 0.001 HIS C5003 PHE 0.012 0.001 PHE D4671 TYR 0.014 0.001 TYR B5009 ARG 0.011 0.001 ARG D4192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 297 time to evaluate : 1.712 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7016 (mtm-85) REVERT: A 4232 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6146 (tm-30) REVERT: A 4674 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: A 4704 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6435 (pt) REVERT: A 5031 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6821 (tt0) REVERT: B 4180 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7016 (mtm-85) REVERT: B 4232 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6145 (tm-30) REVERT: B 4674 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: B 4704 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6437 (pt) REVERT: B 5031 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: C 4180 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7011 (mtm-85) REVERT: C 4232 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6143 (tm-30) REVERT: C 4674 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: C 4704 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6254 (pt) REVERT: C 5031 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: D 4180 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7016 (mtm-85) REVERT: D 4218 ILE cc_start: 0.8180 (pt) cc_final: 0.7780 (mp) REVERT: D 4232 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6140 (tm-30) REVERT: D 4674 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: D 4704 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6255 (pt) REVERT: D 4948 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: D 5031 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6827 (tt0) outliers start: 65 outliers final: 36 residues processed: 341 average time/residue: 1.0403 time to fit residues: 398.3133 Evaluate side-chains 338 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 285 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4236 SER Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4674 GLU Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain A residue 5031 GLN Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4236 SER Chi-restraints excluded: chain B residue 4325 ARG Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4674 GLU Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain B residue 5031 GLN Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4236 SER Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4674 GLU Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain C residue 5031 GLN Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4236 SER Chi-restraints excluded: chain D residue 4325 ARG Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4674 GLU Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4948 GLU Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Chi-restraints excluded: chain D residue 5031 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 111 optimal weight: 0.0570 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4250 GLN B4250 GLN C4250 GLN D4250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16256 Z= 0.235 Angle : 0.541 7.758 22180 Z= 0.279 Chirality : 0.037 0.205 2488 Planarity : 0.004 0.043 2736 Dihedral : 8.985 76.007 2356 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.86 % Allowed : 26.64 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.19), residues: 2008 helix: 2.00 (0.13), residues: 1364 sheet: -0.70 (0.49), residues: 104 loop : -0.59 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A4716 HIS 0.006 0.001 HIS A5003 PHE 0.012 0.001 PHE D4916 TYR 0.019 0.002 TYR B4630 ARG 0.013 0.001 ARG C4192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 277 time to evaluate : 1.656 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7012 (mtm-85) REVERT: A 4232 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6177 (tm-30) REVERT: A 4662 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7642 (t0) REVERT: A 4674 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: A 4704 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6435 (pt) REVERT: A 4778 TRP cc_start: 0.7422 (OUTLIER) cc_final: 0.5971 (t-100) REVERT: A 5031 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6950 (tt0) REVERT: B 4180 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7020 (mtm-85) REVERT: B 4232 GLU cc_start: 0.6627 (mm-30) cc_final: 0.6178 (tm-30) REVERT: B 4662 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7643 (t0) REVERT: B 4674 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: B 4704 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6436 (pt) REVERT: B 4778 TRP cc_start: 0.7419 (OUTLIER) cc_final: 0.5969 (t-100) REVERT: B 5031 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: C 4180 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7021 (mtm-85) REVERT: C 4232 GLU cc_start: 0.6622 (mm-30) cc_final: 0.6174 (tm-30) REVERT: C 4662 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7638 (t0) REVERT: C 4674 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: C 4704 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6347 (pt) REVERT: C 4778 TRP cc_start: 0.7417 (OUTLIER) cc_final: 0.5958 (t-100) REVERT: C 5031 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6893 (tt0) REVERT: D 4180 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7015 (mtm-85) REVERT: D 4232 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6170 (tm-30) REVERT: D 4662 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7645 (t0) REVERT: D 4674 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: D 4704 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6344 (pt) REVERT: D 4778 TRP cc_start: 0.7421 (OUTLIER) cc_final: 0.5961 (t-100) REVERT: D 5031 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6952 (tt0) outliers start: 71 outliers final: 40 residues processed: 327 average time/residue: 1.0545 time to fit residues: 386.4453 Evaluate side-chains 333 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 269 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4236 SER Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4674 GLU Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4778 TRP Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain A residue 5031 GLN Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4236 SER Chi-restraints excluded: chain B residue 4325 ARG Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4674 GLU Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain B residue 4880 MET Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain B residue 5031 GLN Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4236 SER Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4674 GLU Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4778 TRP Chi-restraints excluded: chain C residue 4880 MET Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain C residue 5031 GLN Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4236 SER Chi-restraints excluded: chain D residue 4325 ARG Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4662 ASN Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4674 GLU Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4778 TRP Chi-restraints excluded: chain D residue 4880 MET Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Chi-restraints excluded: chain D residue 5031 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 125 optimal weight: 0.4980 chunk 133 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4250 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16256 Z= 0.254 Angle : 0.560 8.292 22180 Z= 0.288 Chirality : 0.037 0.257 2488 Planarity : 0.004 0.040 2736 Dihedral : 8.769 68.914 2356 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.21 % Allowed : 25.96 % Favored : 68.84 % 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: 1.68 (0.19), residues: 2008 helix: 1.93 (0.13), residues: 1364 sheet: -0.79 (0.49), residues: 104 loop : -0.58 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C4778 HIS 0.007 0.001 HIS B5003 PHE 0.013 0.001 PHE A4237 TYR 0.013 0.001 TYR D4994 ARG 0.012 0.001 ARG B4192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 287 time to evaluate : 1.585 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6972 (mtm-85) REVERT: A 4232 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6180 (tm-30) REVERT: A 4662 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7710 (t0) REVERT: A 4674 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: B 4180 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6991 (mtm-85) REVERT: B 4232 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6184 (tm-30) REVERT: B 4662 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7710 (t0) REVERT: B 4674 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: C 4180 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7009 (mtm-85) REVERT: C 4232 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6194 (tm-30) REVERT: C 4662 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7708 (t0) REVERT: C 4674 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: C 4704 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6303 (pt) REVERT: D 4180 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6973 (mtm-85) REVERT: D 4218 ILE cc_start: 0.8211 (pt) cc_final: 0.7817 (mp) REVERT: D 4232 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6176 (tm-30) REVERT: D 4662 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7710 (t0) REVERT: D 4674 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: D 4704 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6301 (pt) outliers start: 76 outliers final: 39 residues processed: 346 average time/residue: 1.0326 time to fit residues: 402.1165 Evaluate side-chains 329 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 276 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4236 SER Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4674 GLU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4236 SER Chi-restraints excluded: chain B residue 4325 ARG Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4674 GLU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4236 SER Chi-restraints excluded: chain C residue 4558 ASN Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4674 GLU Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4236 SER Chi-restraints excluded: chain D residue 4325 ARG Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4662 ASN Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4674 GLU Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.6980 chunk 171 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 110 optimal weight: 0.0270 chunk 79 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16256 Z= 0.231 Angle : 0.562 8.354 22180 Z= 0.289 Chirality : 0.037 0.244 2488 Planarity : 0.004 0.040 2736 Dihedral : 8.393 69.616 2352 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.52 % Allowed : 26.58 % Favored : 68.90 % 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: 1.68 (0.19), residues: 2008 helix: 1.95 (0.13), residues: 1364 sheet: -0.93 (0.49), residues: 104 loop : -0.58 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B4701 HIS 0.005 0.001 HIS A5003 PHE 0.014 0.001 PHE D4991 TYR 0.013 0.001 TYR D5009 ARG 0.012 0.001 ARG D4192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 294 time to evaluate : 1.709 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6952 (mtm-85) REVERT: A 4232 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6212 (tm-30) REVERT: A 4662 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7705 (t0) REVERT: A 4674 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: B 4180 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6954 (mtm-85) REVERT: B 4232 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6373 (tm-30) REVERT: B 4662 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7708 (t0) REVERT: B 4674 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: C 4180 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6955 (mtm-85) REVERT: C 4232 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6227 (tm-30) REVERT: C 4662 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7705 (t0) REVERT: C 4674 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: C 4704 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6160 (pt) REVERT: D 4180 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6952 (mtm-85) REVERT: D 4218 ILE cc_start: 0.8162 (pt) cc_final: 0.7782 (mp) REVERT: D 4232 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6371 (tm-30) REVERT: D 4662 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7707 (t0) REVERT: D 4674 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: D 4704 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6160 (pt) outliers start: 66 outliers final: 37 residues processed: 340 average time/residue: 1.0224 time to fit residues: 391.1306 Evaluate side-chains 315 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 264 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4236 SER Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4674 GLU Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4236 SER Chi-restraints excluded: chain B residue 4325 ARG Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4674 GLU Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4236 SER Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4674 GLU Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4236 SER Chi-restraints excluded: chain D residue 4325 ARG Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4662 ASN Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4674 GLU Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4880 MET Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 187 optimal weight: 0.3980 chunk 161 optimal weight: 0.0000 chunk 16 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 99 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16256 Z= 0.198 Angle : 0.556 8.365 22180 Z= 0.285 Chirality : 0.036 0.237 2488 Planarity : 0.004 0.046 2736 Dihedral : 8.177 75.387 2344 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.19 % Favored : 97.61 % Rotamer: Outliers : 4.04 % Allowed : 27.12 % Favored : 68.84 % 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: 1.71 (0.19), residues: 2008 helix: 1.97 (0.13), residues: 1364 sheet: -0.93 (0.49), residues: 104 loop : -0.57 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C4205 HIS 0.005 0.001 HIS B5003 PHE 0.047 0.002 PHE D4237 TYR 0.020 0.001 TYR D4630 ARG 0.014 0.001 ARG A4192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 304 time to evaluate : 1.911 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6955 (mtm-85) REVERT: A 4232 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6360 (tm-30) REVERT: A 4649 LEU cc_start: 0.8188 (mm) cc_final: 0.7961 (mp) REVERT: A 4662 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7691 (t0) REVERT: A 4674 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: B 4180 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6958 (mtm-85) REVERT: B 4232 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6319 (tm-30) REVERT: B 4649 LEU cc_start: 0.8192 (mm) cc_final: 0.7966 (mp) REVERT: B 4662 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7642 (t0) REVERT: B 4674 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: C 4180 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6955 (mtm-85) REVERT: C 4232 GLU cc_start: 0.6630 (mm-30) cc_final: 0.6374 (tm-30) REVERT: C 4649 LEU cc_start: 0.8188 (mm) cc_final: 0.7963 (mp) REVERT: C 4662 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7690 (t0) REVERT: C 4674 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: D 4180 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6958 (mtm-85) REVERT: D 4218 ILE cc_start: 0.8172 (pt) cc_final: 0.7782 (mp) REVERT: D 4232 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6312 (tm-30) REVERT: D 4649 LEU cc_start: 0.8193 (mm) cc_final: 0.7969 (mp) REVERT: D 4662 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7643 (t0) REVERT: D 4674 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7999 (tt0) outliers start: 59 outliers final: 40 residues processed: 342 average time/residue: 1.0308 time to fit residues: 396.2104 Evaluate side-chains 341 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 289 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4236 SER Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4674 GLU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4236 SER Chi-restraints excluded: chain B residue 4325 ARG Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4674 GLU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4236 SER Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4674 GLU Chi-restraints excluded: chain C residue 4880 MET Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4236 SER Chi-restraints excluded: chain D residue 4325 ARG Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4662 ASN Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4674 GLU Chi-restraints excluded: chain D residue 4880 MET Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 44 optimal weight: 0.3980 chunk 162 optimal weight: 0.0060 chunk 67 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.180476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.151426 restraints weight = 17686.779| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.37 r_work: 0.3571 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16256 Z= 0.196 Angle : 0.562 8.896 22180 Z= 0.287 Chirality : 0.036 0.233 2488 Planarity : 0.004 0.047 2736 Dihedral : 7.944 80.274 2340 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.99 % Favored : 97.81 % Rotamer: Outliers : 3.70 % Allowed : 28.08 % Favored : 68.22 % 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: 1.74 (0.19), residues: 2008 helix: 1.93 (0.13), residues: 1380 sheet: -0.96 (0.49), residues: 104 loop : -0.43 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C4701 HIS 0.004 0.001 HIS D5003 PHE 0.021 0.001 PHE D4991 TYR 0.013 0.001 TYR D5009 ARG 0.014 0.001 ARG C4192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6428.15 seconds wall clock time: 114 minutes 10.78 seconds (6850.78 seconds total)