Starting phenix.real_space_refine on Sat Mar 16 05:02:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtb_27695/03_2024/8dtb_27695_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtb_27695/03_2024/8dtb_27695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtb_27695/03_2024/8dtb_27695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtb_27695/03_2024/8dtb_27695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtb_27695/03_2024/8dtb_27695_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtb_27695/03_2024/8dtb_27695_updated.pdb" } resolution = 3.14 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= -0.005 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 9053 2.51 5 N 2219 2.21 5 O 2352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 4239": "OE1" <-> "OE2" Residue "G GLU 4244": "OE1" <-> "OE2" Residue "G GLU 4676": "OE1" <-> "OE2" Residue "G GLU 4900": "OE1" <-> "OE2" Residue "G GLU 4902": "OE1" <-> "OE2" Residue "G GLU 4948": "OE1" <-> "OE2" Residue "A GLU 4902": "OE1" <-> "OE2" Residue "D GLU 4239": "OE1" <-> "OE2" Residue "D GLU 4640": "OE1" <-> "OE2" Residue "D GLU 4674": "OE1" <-> "OE2" Residue "D GLU 4676": "OE1" <-> "OE2" Residue "D GLU 4948": "OE1" <-> "OE2" Residue "D GLU 4952": "OE1" <-> "OE2" Residue "J GLU 4239": "OE1" <-> "OE2" Residue "J GLU 4900": "OE1" <-> "OE2" Residue "J GLU 4948": "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: 13724 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 257 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "G" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3344 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 9, 'TRANS': 427} Chain breaks: 4 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 14, 'GLU:plan': 20, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3267 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 9, 'TRANS': 416} Chain breaks: 4 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 143 Chain: "D" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3360 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 426} Chain breaks: 4 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 14, 'GLU:plan': 18, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 149 Chain: "J" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 9, 'TRANS': 423} Chain breaks: 5 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 10, 'GLU:plan': 18, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 151 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.40, per 1000 atoms: 0.54 Number of scatterers: 13724 At special positions: 0 Unit cell: (100.58, 140.17, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 12 15.00 O 2352 8.00 N 2219 7.00 C 9053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 17 " distance=2.03 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 21 " distance=2.01 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 32 " distance=2.06 Simple disulfide: pdb=" SG CYS G4876 " - pdb=" SG CYS G4882 " distance=2.03 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Simple disulfide: pdb=" SG CYS J4876 " - pdb=" SG CYS J4882 " distance=2.04 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: 5.76 Conformation dependent library (CDL) restraints added in 2.5 seconds 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 4 sheets defined 68.8% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'G' and resid 4209 through 4224 Processing helix chain 'G' and resid 4230 through 4251 Processing helix chain 'G' and resid 4324 through 4341 Processing helix chain 'G' and resid 4542 through 4557 removed outlier: 4.266A pdb=" N VAL G4546 " --> pdb=" O GLY G4542 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN G4547 " --> pdb=" O GLU G4543 " (cutoff:3.500A) Processing helix chain 'G' and resid 4559 through 4579 removed outlier: 4.346A pdb=" N PHE G4579 " --> pdb=" O PHE G4575 " (cutoff:3.500A) Processing helix chain 'G' and resid 4640 through 4664 removed outlier: 3.683A pdb=" N LEU G4648 " --> pdb=" O TRP G4644 " (cutoff:3.500A) Processing helix chain 'G' and resid 4666 through 4682 Processing helix chain 'G' and resid 4686 through 4689 No H-bonds generated for 'chain 'G' and resid 4686 through 4689' Processing helix chain 'G' and resid 4697 through 4705 removed outlier: 3.961A pdb=" N ARG G4703 " --> pdb=" O GLY G4699 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU G4704 " --> pdb=" O GLN G4700 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL G4705 " --> pdb=" O TRP G4701 " (cutoff:3.500A) Processing helix chain 'G' and resid 4720 through 4727 Processing helix chain 'G' and resid 4734 through 4741 Processing helix chain 'G' and resid 4767 through 4770 No H-bonds generated for 'chain 'G' and resid 4767 through 4770' Processing helix chain 'G' and resid 4773 through 4785 Processing helix chain 'G' and resid 4787 through 4805 removed outlier: 3.826A pdb=" N HIS G4803 " --> pdb=" O SER G4799 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR G4804 " --> pdb=" O LEU G4800 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN G4805 " --> pdb=" O LEU G4801 " (cutoff:3.500A) Processing helix chain 'G' and resid 4808 through 4819 Processing helix chain 'G' and resid 4821 through 4832 removed outlier: 3.875A pdb=" N VAL G4830 " --> pdb=" O ILE G4826 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR G4831 " --> pdb=" O LEU G4827 " (cutoff:3.500A) Processing helix chain 'G' and resid 4834 through 4857 Processing helix chain 'G' and resid 4879 through 4888 Processing helix chain 'G' and resid 4890 through 4893 No H-bonds generated for 'chain 'G' and resid 4890 through 4893' Processing helix chain 'G' and resid 4910 through 4925 Processing helix chain 'G' and resid 4928 through 4955 Processing helix chain 'A' and resid 4210 through 4223 Processing helix chain 'A' and resid 4230 through 4250 removed outlier: 4.386A pdb=" N PHE A4243 " --> pdb=" O GLU A4239 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A4244 " --> pdb=" O ASP A4240 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A4245 " --> pdb=" O THR A4241 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A4246 " --> pdb=" O ILE A4242 " (cutoff:3.500A) Processing helix chain 'A' and resid 4324 through 4341 Processing helix chain 'A' and resid 4553 through 4557 removed outlier: 3.705A pdb=" N ARG A4557 " --> pdb=" O ASN A4553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4553 through 4557' Processing helix chain 'A' and resid 4559 through 4579 removed outlier: 3.655A pdb=" N LEU A4578 " --> pdb=" O ASN A4574 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4639 through 4664 removed outlier: 3.903A pdb=" N ASN A4662 " --> pdb=" O ILE A4658 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS A4663 " --> pdb=" O ILE A4659 " (cutoff:3.500A) Processing helix chain 'A' and resid 4666 through 4683 Processing helix chain 'A' and resid 4697 through 4707 removed outlier: 3.637A pdb=" N ARG A4703 " --> pdb=" O GLY A4699 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4711 through 4713 No H-bonds generated for 'chain 'A' and resid 4711 through 4713' Processing helix chain 'A' and resid 4721 through 4727 removed outlier: 3.668A pdb=" N LEU A4725 " --> pdb=" O LYS A4721 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP A4726 " --> pdb=" O ARG A4722 " (cutoff:3.500A) Processing helix chain 'A' and resid 4734 through 4740 Processing helix chain 'A' and resid 4773 through 4785 Processing helix chain 'A' and resid 4787 through 4804 removed outlier: 3.785A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4819 removed outlier: 3.652A pdb=" N ILE A4816 " --> pdb=" O LEU A4813 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 4.038A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR A4831 " --> pdb=" O LEU A4827 " (cutoff:3.500A) Processing helix chain 'A' and resid 4834 through 4857 Processing helix chain 'A' and resid 4879 through 4893 removed outlier: 4.113A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4897 through 4899 No H-bonds generated for 'chain 'A' and resid 4897 through 4899' Processing helix chain 'A' and resid 4910 through 4924 Processing helix chain 'A' and resid 4928 through 4954 removed outlier: 3.769A pdb=" N GLN A4947 " --> pdb=" O LEU A4943 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A4948 " --> pdb=" O ARG A4944 " (cutoff:3.500A) Processing helix chain 'A' and resid 4965 through 4968 No H-bonds generated for 'chain 'A' and resid 4965 through 4968' Processing helix chain 'D' and resid 4209 through 4223 Processing helix chain 'D' and resid 4230 through 4251 removed outlier: 3.527A pdb=" N PHE D4243 " --> pdb=" O GLU D4239 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN D4246 " --> pdb=" O ILE D4242 " (cutoff:3.500A) Processing helix chain 'D' and resid 4324 through 4340 Processing helix chain 'D' and resid 4542 through 4578 removed outlier: 3.894A pdb=" N ASN D4558 " --> pdb=" O TYR D4554 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE D4559 " --> pdb=" O LEU D4555 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR D4560 " --> pdb=" O SER D4556 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR D4561 " --> pdb=" O ARG D4557 " (cutoff:3.500A) Processing helix chain 'D' and resid 4637 through 4664 removed outlier: 3.586A pdb=" N GLU D4640 " --> pdb=" O GLY D4637 " (cutoff:3.500A) Proline residue: D4641 - end of helix removed outlier: 3.517A pdb=" N LEU D4648 " --> pdb=" O CYS D4645 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D4664 " --> pdb=" O TYR D4661 " (cutoff:3.500A) Processing helix chain 'D' and resid 4666 through 4683 Processing helix chain 'D' and resid 4697 through 4705 removed outlier: 4.226A pdb=" N ARG D4703 " --> pdb=" O GLY D4699 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) Processing helix chain 'D' and resid 4720 through 4727 Processing helix chain 'D' and resid 4734 through 4741 Processing helix chain 'D' and resid 4774 through 4785 Processing helix chain 'D' and resid 4787 through 4804 removed outlier: 3.926A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4819 removed outlier: 3.932A pdb=" N PHE D4809 " --> pdb=" O ASN D4806 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D4810 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D4811 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP D4815 " --> pdb=" O HIS D4812 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D4816 " --> pdb=" O LEU D4813 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.856A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR D4831 " --> pdb=" O LEU D4827 " (cutoff:3.500A) Processing helix chain 'D' and resid 4834 through 4857 removed outlier: 3.567A pdb=" N VAL D4854 " --> pdb=" O LEU D4850 " (cutoff:3.500A) Processing helix chain 'D' and resid 4879 through 4888 Processing helix chain 'D' and resid 4890 through 4893 No H-bonds generated for 'chain 'D' and resid 4890 through 4893' Processing helix chain 'D' and resid 4910 through 4924 Processing helix chain 'D' and resid 4928 through 4955 removed outlier: 3.746A pdb=" N ILE D4936 " --> pdb=" O ILE D4932 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA D4939 " --> pdb=" O LEU D4935 " (cutoff:3.500A) Processing helix chain 'D' and resid 4965 through 4968 No H-bonds generated for 'chain 'D' and resid 4965 through 4968' Processing helix chain 'J' and resid 4209 through 4223 Processing helix chain 'J' and resid 4230 through 4251 removed outlier: 3.682A pdb=" N PHE J4243 " --> pdb=" O GLU J4239 " (cutoff:3.500A) Processing helix chain 'J' and resid 4324 through 4340 Processing helix chain 'J' and resid 4542 through 4557 Processing helix chain 'J' and resid 4560 through 4579 removed outlier: 4.115A pdb=" N PHE J4579 " --> pdb=" O PHE J4575 " (cutoff:3.500A) Processing helix chain 'J' and resid 4638 through 4664 removed outlier: 3.523A pdb=" N ALA J4642 " --> pdb=" O TYR J4638 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP J4644 " --> pdb=" O GLU J4640 " (cutoff:3.500A) Processing helix chain 'J' and resid 4666 through 4683 Processing helix chain 'J' and resid 4697 through 4707 removed outlier: 4.556A pdb=" N LEU J4704 " --> pdb=" O GLN J4700 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL J4705 " --> pdb=" O TRP J4701 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU J4706 " --> pdb=" O ASP J4702 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN J4707 " --> pdb=" O ARG J4703 " (cutoff:3.500A) Processing helix chain 'J' and resid 4720 through 4727 Processing helix chain 'J' and resid 4734 through 4741 removed outlier: 3.994A pdb=" N LEU J4740 " --> pdb=" O ARG J4736 " (cutoff:3.500A) Processing helix chain 'J' and resid 4773 through 4785 Processing helix chain 'J' and resid 4787 through 4804 removed outlier: 3.948A pdb=" N HIS J4803 " --> pdb=" O SER J4799 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TYR J4804 " --> pdb=" O LEU J4800 " (cutoff:3.500A) Processing helix chain 'J' and resid 4806 through 4819 removed outlier: 3.550A pdb=" N PHE J4809 " --> pdb=" O ASN J4806 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA J4811 " --> pdb=" O PHE J4808 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J4813 " --> pdb=" O ALA J4810 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU J4814 " --> pdb=" O ALA J4811 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP J4815 " --> pdb=" O HIS J4812 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE J4816 " --> pdb=" O LEU J4813 " (cutoff:3.500A) Processing helix chain 'J' and resid 4821 through 4832 removed outlier: 3.914A pdb=" N VAL J4830 " --> pdb=" O ILE J4826 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR J4831 " --> pdb=" O LEU J4827 " (cutoff:3.500A) Processing helix chain 'J' and resid 4834 through 4857 Processing helix chain 'J' and resid 4879 through 4893 removed outlier: 3.992A pdb=" N VAL J4891 " --> pdb=" O MET J4887 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG J4892 " --> pdb=" O TYR J4888 " (cutoff:3.500A) Processing helix chain 'J' and resid 4897 through 4899 No H-bonds generated for 'chain 'J' and resid 4897 through 4899' Processing helix chain 'J' and resid 4910 through 4924 Processing helix chain 'J' and resid 4928 through 4956 Processing helix chain 'J' and resid 4965 through 4968 No H-bonds generated for 'chain 'J' and resid 4965 through 4968' Processing sheet with id= A, first strand: chain 'G' and resid 4580 through 4583 Processing sheet with id= B, first strand: chain 'A' and resid 4580 through 4583 removed outlier: 3.669A pdb=" N SER A4583 " --> pdb=" O VAL A4628 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 4580 through 4583 Processing sheet with id= D, first strand: chain 'J' and resid 4580 through 4583 828 hydrogen bonds defined for protein. 2325 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: 3.80 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2480 1.33 - 1.45: 3780 1.45 - 1.57: 7644 1.57 - 1.70: 21 1.70 - 1.82: 138 Bond restraints: 14063 Sorted by residual: bond pdb=" C ILE G4932 " pdb=" O ILE G4932 " ideal model delta sigma weight residual 1.237 1.297 -0.060 1.12e-02 7.97e+03 2.89e+01 bond pdb=" N GLN A4691 " pdb=" CA GLN A4691 " ideal model delta sigma weight residual 1.458 1.490 -0.032 7.40e-03 1.83e+04 1.91e+01 bond pdb=" C TYR D4638 " pdb=" N MET D4639 " ideal model delta sigma weight residual 1.333 1.287 0.046 1.43e-02 4.89e+03 1.03e+01 bond pdb=" N ILE G4936 " pdb=" CA ILE G4936 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N ILE G4932 " pdb=" CA ILE G4932 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.18e+00 ... (remaining 14058 not shown) Histogram of bond angle deviations from ideal: 99.76 - 107.78: 424 107.78 - 115.81: 8243 115.81 - 123.83: 10121 123.83 - 131.85: 290 131.85 - 139.87: 36 Bond angle restraints: 19114 Sorted by residual: angle pdb=" C CYS B 21 " pdb=" CA CYS B 21 " pdb=" CB CYS B 21 " ideal model delta sigma weight residual 111.74 102.14 9.60 1.37e+00 5.33e-01 4.91e+01 angle pdb=" N ALA D4939 " pdb=" CA ALA D4939 " pdb=" C ALA D4939 " ideal model delta sigma weight residual 111.11 117.90 -6.79 1.20e+00 6.94e-01 3.20e+01 angle pdb=" C PRO A4692 " pdb=" CA PRO A4692 " pdb=" CB PRO A4692 " ideal model delta sigma weight residual 112.64 104.57 8.07 1.43e+00 4.89e-01 3.18e+01 angle pdb=" N GLN G4933 " pdb=" CA GLN G4933 " pdb=" C GLN G4933 " ideal model delta sigma weight residual 111.28 106.36 4.92 1.09e+00 8.42e-01 2.04e+01 angle pdb=" CA ILE G4931 " pdb=" C ILE G4931 " pdb=" O ILE G4931 " ideal model delta sigma weight residual 120.85 116.30 4.55 1.06e+00 8.90e-01 1.84e+01 ... (remaining 19109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6855 17.70 - 35.40: 906 35.40 - 53.11: 310 53.11 - 70.81: 45 70.81 - 88.51: 15 Dihedral angle restraints: 8131 sinusoidal: 3000 harmonic: 5131 Sorted by residual: dihedral pdb=" CB CYS B 10 " pdb=" SG CYS B 10 " pdb=" SG CYS B 21 " pdb=" CB CYS B 21 " ideal model delta sinusoidal sigma weight residual 93.00 -178.93 -88.07 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 32 " pdb=" CB CYS B 32 " ideal model delta sinusoidal sigma weight residual -86.00 -121.70 35.70 1 1.00e+01 1.00e-02 1.80e+01 dihedral pdb=" CB CYS B 3 " pdb=" SG CYS B 3 " pdb=" SG CYS B 17 " pdb=" CB CYS B 17 " ideal model delta sinusoidal sigma weight residual -86.00 -119.45 33.45 1 1.00e+01 1.00e-02 1.59e+01 ... (remaining 8128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1952 0.061 - 0.123: 196 0.123 - 0.184: 20 0.184 - 0.245: 5 0.245 - 0.307: 1 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CG LEU A4331 " pdb=" CB LEU A4331 " pdb=" CD1 LEU A4331 " pdb=" CD2 LEU A4331 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ILE D4937 " pdb=" N ILE D4937 " pdb=" C ILE D4937 " pdb=" CB ILE D4937 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA CYS B 21 " pdb=" N CYS B 21 " pdb=" C CYS B 21 " pdb=" CB CYS B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2171 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D4637 " 0.020 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C GLY D4637 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY D4637 " 0.028 2.00e-02 2.50e+03 pdb=" N TYR D4638 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN G4691 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.81e+00 pdb=" N PRO G4692 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO G4692 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G4692 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY G4637 " -0.013 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C GLY G4637 " 0.048 2.00e-02 2.50e+03 pdb=" O GLY G4637 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR G4638 " -0.016 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 417 2.72 - 3.26: 14020 3.26 - 3.81: 22934 3.81 - 4.35: 26129 4.35 - 4.90: 44864 Nonbonded interactions: 108364 Sorted by model distance: nonbonded pdb=" OG1 THR G4689 " pdb=" OE1 GLU G4690 " model vdw 2.175 2.440 nonbonded pdb=" OH TYR D4687 " pdb=" O GLY D4699 " model vdw 2.203 2.440 nonbonded pdb=" O GLU J4952 " pdb=" OG1 THR J4956 " model vdw 2.215 2.440 nonbonded pdb=" O GLY A4781 " pdb=" OG1 THR A4785 " model vdw 2.225 2.440 nonbonded pdb=" O ALA J4248 " pdb=" OG SER J4252 " model vdw 2.233 2.440 ... (remaining 108359 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' and (resid 4208 or (resid 4209 and (name N or name CA or name C or na \ me O or name CB )) or resid 4210 or (resid 4211 through 4212 and (name N or name \ CA or name C or name O or name CB )) or resid 4213 through 4219 or (resid 4220 \ and (name N or name CA or name C or name O or name CB )) or resid 4221 through 4 \ 551 or (resid 4552 and (name N or name CA or name C or name O or name CB )) or r \ esid 4553 through 4690 or (resid 4691 and (name N or name CA or name C or name O \ or name CB )) or resid 4692 or resid 4696 through 4697 or (resid 4698 and (name \ N or name CA or name C or name O or name CB )) or resid 4699 through 4725 or (r \ esid 4726 through 4727 and (name N or name CA or name C or name O or name CB )) \ or resid 4728 through 4736 or (resid 4737 through 4739 and (name N or name CA or \ name C or name O or name CB )) or resid 4740 through 4742 or resid 4769 through \ 4785 or (resid 4786 and (name N or name CA or name C or name O or name CB )) or \ resid 4787 through 4965 or (resid 4966 and (name N or name CA or name C or name \ O or name CB )) or resid 4967 through 4968 or resid 5103)) selection = (chain 'D' and (resid 4208 through 4210 or (resid 4211 through 4212 and (name N \ or name CA or name C or name O or name CB )) or resid 4213 through 4223 or (resi \ d 4224 and (name N or name CA or name C or name O or name CB )) or resid 4225 th \ rough 4243 or (resid 4244 and (name N or name CA or name C or name O or name CB \ )) or resid 4245 through 4251 or resid 4323 through 4340 or (resid 4341 through \ 4342 and (name N or name CA or name C or name O or name CB )) or resid 4343 thro \ ugh 4344 or resid 4549 through 4551 or (resid 4552 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4553 through 4639 or (resid 4640 and (name \ N or name CA or name C or name O or name CB )) or resid 4641 through 4679 or (re \ sid 4680 and (name N or name CA or name C or name O or name CB )) or resid 4681 \ through 4689 or (resid 4690 through 4691 and (name N or name CA or name C or nam \ e O or name CB )) or resid 4692 or resid 4696 through 4717 or (resid 4718 and (n \ ame N or name CA or name C or name O or name CB )) or resid 4719 through 4721 or \ (resid 4722 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 723 through 4725 or (resid 4726 through 4727 and (name N or name CA or name C or \ name O or name CB )) or resid 4728 through 4730 or (resid 4731 and (name N or n \ ame CA or name C or name O or name CB )) or resid 4732 through 4733 or (resid 47 \ 34 through 4739 and (name N or name CA or name C or name O or name CB )) or resi \ d 4740 through 4742 or (resid 4769 through 4772 and (name N or name CA or name C \ or name O or name CB )) or resid 4773 through 4785 or (resid 4786 and (name N o \ r name CA or name C or name O or name CB )) or resid 4787 through 4820 or (resid \ 4821 and (name N or name CA or name C or name O or name CB )) or resid 4822 thr \ ough 4956 or (resid 4957 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4958 through 4968 or resid 5104)) selection = (chain 'G' and (resid 4208 or (resid 4209 and (name N or name CA or name C or na \ me O or name CB )) or resid 4210 or (resid 4211 through 4212 and (name N or name \ CA or name C or name O or name CB )) or resid 4213 through 4243 or (resid 4244 \ and (name N or name CA or name C or name O or name CB )) or resid 4245 through 4 \ 251 or resid 4323 through 4340 or (resid 4341 through 4342 and (name N or name C \ A or name C or name O or name CB )) or resid 4343 through 4344 or resid 4549 thr \ ough 4551 or (resid 4552 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4553 through 4679 or (resid 4680 and (name N or name CA or name C or \ name O or name CB )) or resid 4681 through 4689 or (resid 4690 through 4691 and \ (name N or name CA or name C or name O or name CB )) or resid 4692 or resid 4696 \ through 4702 or (resid 4703 and (name N or name CA or name C or name O or name \ CB )) or resid 4704 through 4721 or (resid 4722 and (name N or name CA or name C \ or name O or name CB )) or resid 4723 through 4742 or (resid 4769 through 4772 \ and (name N or name CA or name C or name O or name CB )) or resid 4773 through 4 \ 820 or (resid 4821 and (name N or name CA or name C or name O or name CB )) or r \ esid 4822 through 4965 or (resid 4966 and (name N or name CA or name C or name O \ or name CB )) or resid 4967 through 4968 or resid 5301)) selection = (chain 'J' and (resid 4208 or (resid 4209 and (name N or name CA or name C or na \ me O or name CB )) or resid 4210 through 4211 or (resid 4212 and (name N or name \ CA or name C or name O or name CB )) or resid 4213 through 4219 or (resid 4220 \ and (name N or name CA or name C or name O or name CB )) or resid 4221 through 4 \ 223 or (resid 4224 and (name N or name CA or name C or name O or name CB )) or r \ esid 4225 through 4243 or (resid 4244 and (name N or name CA or name C or name O \ or name CB )) or resid 4245 through 4251 or resid 4323 through 4340 or (resid 4 \ 341 through 4342 and (name N or name CA or name C or name O or name CB )) or res \ id 4343 through 4344 or resid 4549 through 4679 or (resid 4680 and (name N or na \ me CA or name C or name O or name CB )) or resid 4681 through 4697 or (resid 469 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 4699 through \ 4721 or (resid 4722 and (name N or name CA or name C or name O or name CB )) or \ resid 4723 through 4725 or (resid 4726 through 4727 and (name N or name CA or n \ ame C or name O or name CB )) or resid 4728 through 4736 or (resid 4737 through \ 4739 and (name N or name CA or name C or name O or name CB )) or resid 4740 thro \ ugh 4742 or (resid 4769 through 4772 and (name N or name CA or name C or name O \ or name CB )) or resid 4773 or (resid 4774 and (name N or name CA or name C or n \ ame O or name CB )) or resid 4775 through 4785 or (resid 4786 and (name N or nam \ e CA or name C or name O or name CB )) or resid 4787 through 4820 or (resid 4821 \ and (name N or name CA or name C or name O or name CB )) or resid 4822 through \ 4954 or (resid 4955 and (name N or name CA or name C or name O or name CB )) or \ resid 4956 through 4968 or resid 5105)) } 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: 7.460 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: 0.000 Extract box with map and model: 18.590 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.820 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 14063 Z= 0.218 Angle : 0.619 9.712 19114 Z= 0.376 Chirality : 0.039 0.307 2174 Planarity : 0.004 0.070 2340 Dihedral : 18.081 88.510 4806 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.99 % Allowed : 28.96 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1721 helix: 1.71 (0.15), residues: 1209 sheet: -0.30 (0.77), residues: 42 loop : -1.62 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D4794 HIS 0.007 0.000 HIS G4728 PHE 0.036 0.001 PHE J4671 TYR 0.016 0.001 TYR J4851 ARG 0.007 0.000 ARG D4679 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 358 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 4551 PHE cc_start: 0.7247 (m-10) cc_final: 0.6752 (m-10) REVERT: G 4638 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5260 (m-80) REVERT: A 4698 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8102 (mtmm) REVERT: D 4849 TYR cc_start: 0.8475 (t80) cc_final: 0.7992 (t80) REVERT: J 4862 PHE cc_start: 0.5488 (m-10) cc_final: 0.5043 (m-80) REVERT: J 4900 GLU cc_start: 0.7742 (mp0) cc_final: 0.7455 (mp0) outliers start: 13 outliers final: 7 residues processed: 366 average time/residue: 0.2385 time to fit residues: 128.2456 Evaluate side-chains 359 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 350 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain A residue 4231 MET Chi-restraints excluded: chain A residue 4688 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4698 LYS Chi-restraints excluded: chain J residue 4704 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4691 GLN A4714 ASN ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4803 HIS J4707 ASN J4857 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14063 Z= 0.214 Angle : 0.497 6.014 19114 Z= 0.272 Chirality : 0.036 0.141 2174 Planarity : 0.004 0.060 2340 Dihedral : 8.659 84.762 2047 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.32 % Allowed : 23.50 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1721 helix: 1.59 (0.15), residues: 1201 sheet: -0.13 (0.84), residues: 42 loop : -1.40 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A4701 HIS 0.006 0.001 HIS G4728 PHE 0.030 0.002 PHE J4671 TYR 0.016 0.001 TYR D4629 ARG 0.006 0.001 ARG D4679 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 374 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 4638 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5379 (p90) REVERT: G 4740 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8033 (tp) REVERT: G 4948 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 4234 PHE cc_start: 0.7712 (t80) cc_final: 0.7446 (t80) REVERT: A 4557 ARG cc_start: 0.6946 (ptt90) cc_final: 0.6742 (ptt90) REVERT: A 4571 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: A 4681 LEU cc_start: 0.7141 (mp) cc_final: 0.6929 (mt) REVERT: A 4698 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8045 (mtmm) REVERT: D 4676 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: D 4796 MET cc_start: 0.8302 (tpp) cc_final: 0.8065 (tpt) REVERT: J 4242 ILE cc_start: 0.8187 (mt) cc_final: 0.7980 (mp) outliers start: 57 outliers final: 30 residues processed: 405 average time/residue: 0.2314 time to fit residues: 138.4755 Evaluate side-chains 375 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 340 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain G residue 4239 GLU Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4556 SER Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4740 LEU Chi-restraints excluded: chain G residue 4771 ILE Chi-restraints excluded: chain G residue 4779 LYS Chi-restraints excluded: chain G residue 4797 VAL Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4881 THR Chi-restraints excluded: chain A residue 4556 SER Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4688 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4698 LYS Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4741 LEU Chi-restraints excluded: chain D residue 4245 MET Chi-restraints excluded: chain D residue 4657 CYS Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4221 VAL Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4806 ASN Chi-restraints excluded: chain J residue 4853 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4864 ASN ** D4246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J4707 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14063 Z= 0.305 Angle : 0.558 6.837 19114 Z= 0.305 Chirality : 0.038 0.138 2174 Planarity : 0.004 0.066 2340 Dihedral : 7.724 88.424 2030 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 6.75 % Allowed : 23.28 % Favored : 69.98 % 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: 0.53 (0.20), residues: 1721 helix: 1.17 (0.15), residues: 1185 sheet: -0.44 (0.85), residues: 42 loop : -1.54 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J4716 HIS 0.006 0.001 HIS G4728 PHE 0.044 0.002 PHE J4671 TYR 0.019 0.002 TYR A4630 ARG 0.009 0.001 ARG J4215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 365 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 4252 SER cc_start: 0.8541 (t) cc_final: 0.8268 (m) REVERT: G 4555 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8681 (tt) REVERT: G 4558 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8101 (p0) REVERT: G 4638 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.5608 (p90) REVERT: G 4780 PHE cc_start: 0.7052 (m-10) cc_final: 0.6739 (m-10) REVERT: A 4234 PHE cc_start: 0.7757 (t80) cc_final: 0.7544 (t80) REVERT: A 4557 ARG cc_start: 0.7398 (ptt90) cc_final: 0.7129 (ptt90) REVERT: A 4571 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: A 4681 LEU cc_start: 0.7603 (mp) cc_final: 0.7391 (mt) REVERT: A 4701 TRP cc_start: 0.7506 (t-100) cc_final: 0.7284 (t-100) REVERT: A 4796 MET cc_start: 0.7749 (tpt) cc_final: 0.7314 (ttt) REVERT: A 4877 ASP cc_start: 0.7621 (m-30) cc_final: 0.7293 (t0) REVERT: A 4949 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7222 (mm110) REVERT: D 4242 ILE cc_start: 0.8927 (mt) cc_final: 0.8720 (mp) REVERT: D 4564 PHE cc_start: 0.8388 (t80) cc_final: 0.8177 (t80) REVERT: D 4676 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: D 4682 GLU cc_start: 0.7422 (pt0) cc_final: 0.7035 (pt0) REVERT: D 4798 MET cc_start: 0.8468 (tpp) cc_final: 0.8020 (mmt) REVERT: D 4808 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7845 (t80) REVERT: D 4839 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7686 (mtp) REVERT: D 4859 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7628 (p90) REVERT: J 4575 PHE cc_start: 0.8172 (t80) cc_final: 0.7918 (t80) REVERT: J 4683 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: J 4796 MET cc_start: 0.7740 (tpt) cc_final: 0.7136 (tpt) REVERT: J 4818 MET cc_start: 0.7789 (mmt) cc_final: 0.7475 (ttt) outliers start: 89 outliers final: 53 residues processed: 429 average time/residue: 0.2444 time to fit residues: 153.0304 Evaluate side-chains 412 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 350 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain G residue 4213 SER Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4555 LEU Chi-restraints excluded: chain G residue 4556 SER Chi-restraints excluded: chain G residue 4558 ASN Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain G residue 4664 LEU Chi-restraints excluded: chain G residue 4697 VAL Chi-restraints excluded: chain G residue 4710 SER Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4771 ILE Chi-restraints excluded: chain G residue 4801 LEU Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4829 SER Chi-restraints excluded: chain G residue 4831 THR Chi-restraints excluded: chain G residue 4881 THR Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4573 ILE Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4688 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4726 ASP Chi-restraints excluded: chain A residue 4741 LEU Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4797 VAL Chi-restraints excluded: chain A residue 4799 SER Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain D residue 4657 CYS Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4687 TYR Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4808 PHE Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4213 SER Chi-restraints excluded: chain J residue 4221 VAL Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4573 ILE Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4628 VAL Chi-restraints excluded: chain J residue 4664 LEU Chi-restraints excluded: chain J residue 4666 VAL Chi-restraints excluded: chain J residue 4683 PHE Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4707 ASN Chi-restraints excluded: chain J residue 4708 THR Chi-restraints excluded: chain J residue 4732 PHE Chi-restraints excluded: chain J residue 4773 VAL Chi-restraints excluded: chain J residue 4820 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 158 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 chunk 140 optimal weight: 0.9980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4864 ASN ** D4246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J4707 ASN J4803 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14063 Z= 0.215 Angle : 0.501 8.705 19114 Z= 0.269 Chirality : 0.036 0.135 2174 Planarity : 0.004 0.068 2340 Dihedral : 7.405 88.454 2026 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.08 % Allowed : 25.47 % Favored : 69.45 % 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: 0.76 (0.20), residues: 1721 helix: 1.35 (0.15), residues: 1171 sheet: -0.42 (0.87), residues: 42 loop : -1.40 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J4701 HIS 0.006 0.001 HIS G4728 PHE 0.031 0.001 PHE J4671 TYR 0.019 0.001 TYR A4630 ARG 0.004 0.000 ARG J4215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 368 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 4252 SER cc_start: 0.8556 (t) cc_final: 0.8282 (m) REVERT: A 4557 ARG cc_start: 0.7435 (ptt90) cc_final: 0.7112 (ptt90) REVERT: A 4571 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: A 4681 LEU cc_start: 0.7602 (mp) cc_final: 0.7400 (mt) REVERT: A 4701 TRP cc_start: 0.7518 (t-100) cc_final: 0.7301 (t-100) REVERT: A 4796 MET cc_start: 0.7740 (tpt) cc_final: 0.7300 (ttt) REVERT: A 4877 ASP cc_start: 0.7601 (m-30) cc_final: 0.7181 (t0) REVERT: A 4949 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7213 (mm110) REVERT: D 4242 ILE cc_start: 0.8847 (mt) cc_final: 0.8442 (mt) REVERT: D 4676 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: D 4682 GLU cc_start: 0.7384 (pt0) cc_final: 0.6911 (pt0) REVERT: D 4798 MET cc_start: 0.8551 (tpp) cc_final: 0.8126 (mmt) REVERT: D 4808 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7962 (t80) REVERT: D 4859 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7597 (p90) REVERT: D 4873 ASP cc_start: 0.7781 (t0) cc_final: 0.7472 (t0) REVERT: J 4796 MET cc_start: 0.7638 (tpt) cc_final: 0.7038 (tpt) REVERT: J 4818 MET cc_start: 0.7764 (mmt) cc_final: 0.7562 (ttt) outliers start: 67 outliers final: 43 residues processed: 413 average time/residue: 0.2391 time to fit residues: 144.2986 Evaluate side-chains 397 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 350 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain G residue 4213 SER Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4556 SER Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain G residue 4664 LEU Chi-restraints excluded: chain G residue 4697 VAL Chi-restraints excluded: chain G residue 4710 SER Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4771 ILE Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4829 SER Chi-restraints excluded: chain G residue 4881 THR Chi-restraints excluded: chain G residue 4903 ASP Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4966 ASP Chi-restraints excluded: chain G residue 4968 PHE Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4741 LEU Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4828 SER Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain D residue 4657 CYS Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4807 PHE Chi-restraints excluded: chain D residue 4808 PHE Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4628 VAL Chi-restraints excluded: chain J residue 4651 THR Chi-restraints excluded: chain J residue 4662 ASN Chi-restraints excluded: chain J residue 4664 LEU Chi-restraints excluded: chain J residue 4683 PHE Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4717 ASP Chi-restraints excluded: chain J residue 4732 PHE Chi-restraints excluded: chain J residue 4773 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.2826 > 50: distance: 68 - 85: 5.981 distance: 72 - 94: 8.708 distance: 76 - 98: 5.017 distance: 80 - 85: 4.645 distance: 81 - 106: 5.420 distance: 86 - 87: 3.281 distance: 87 - 88: 4.390 distance: 88 - 114: 18.901 distance: 89 - 90: 3.154 distance: 90 - 91: 3.314 distance: 91 - 93: 6.584 distance: 94 - 95: 6.635 distance: 95 - 96: 5.317 distance: 96 - 97: 7.719 distance: 96 - 98: 8.547 distance: 97 - 122: 31.552 distance: 98 - 99: 4.774 distance: 99 - 100: 4.261 distance: 99 - 102: 4.094 distance: 100 - 101: 5.984 distance: 101 - 130: 15.917 distance: 102 - 103: 5.214 distance: 103 - 104: 9.147 distance: 103 - 105: 5.298 distance: 106 - 107: 9.139 distance: 107 - 108: 5.533 distance: 107 - 110: 8.218 distance: 108 - 109: 3.851 distance: 108 - 114: 4.864 distance: 109 - 135: 22.767 distance: 110 - 111: 4.673 distance: 110 - 112: 6.243 distance: 111 - 113: 7.300 distance: 114 - 115: 5.674 distance: 115 - 116: 13.437 distance: 115 - 118: 7.277 distance: 116 - 117: 11.020 distance: 116 - 122: 24.763 distance: 117 - 146: 8.526 distance: 118 - 119: 9.659 distance: 118 - 120: 20.837 distance: 119 - 121: 6.021 distance: 122 - 123: 48.298 distance: 123 - 124: 5.339 distance: 123 - 126: 15.100 distance: 124 - 125: 10.478 distance: 124 - 130: 14.740 distance: 125 - 150: 14.260 distance: 126 - 127: 24.520 distance: 127 - 128: 24.377 distance: 127 - 129: 36.651 distance: 130 - 131: 3.822 distance: 131 - 132: 5.289 distance: 131 - 134: 3.364 distance: 132 - 133: 4.131 distance: 132 - 135: 4.400 distance: 133 - 159: 6.070 distance: 136 - 137: 4.438 distance: 136 - 139: 7.155 distance: 137 - 146: 3.519 distance: 138 - 167: 8.110 distance: 140 - 141: 4.013 distance: 143 - 145: 3.517 distance: 144 - 145: 3.696 distance: 146 - 147: 12.264 distance: 147 - 148: 4.386 distance: 148 - 149: 7.557 distance: 148 - 150: 5.717 distance: 149 - 175: 11.271 distance: 151 - 152: 4.542 distance: 151 - 154: 3.476 distance: 152 - 153: 5.326 distance: 153 - 183: 5.586 distance: 155 - 156: 7.400 distance: 156 - 157: 5.045 distance: 156 - 158: 6.027