Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:17:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/12_2022/6vxm_21444_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/12_2022/6vxm_21444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/12_2022/6vxm_21444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/12_2022/6vxm_21444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/12_2022/6vxm_21444_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/12_2022/6vxm_21444_updated_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D ARG 444": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "E ARG 265": "NH1" <-> "NH2" Residue "E ARG 342": "NH1" <-> "NH2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "E ARG 460": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F ARG 342": "NH1" <-> "NH2" Residue "F ARG 426": "NH1" <-> "NH2" Residue "F ARG 444": "NH1" <-> "NH2" Residue "F ARG 460": "NH1" <-> "NH2" Residue "G ARG 265": "NH1" <-> "NH2" Residue "G ARG 342": "NH1" <-> "NH2" Residue "G ARG 426": "NH1" <-> "NH2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "G ARG 460": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 15064 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "B" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "C" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "D" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "E" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "F" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "G" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Time building chain proxies: 9.13, per 1000 atoms: 0.61 Number of scatterers: 15064 At special positions: 0 Unit cell: (102.3, 102.3, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2716 8.00 N 2485 7.00 C 9779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.37 Conformation dependent library (CDL) restraints added in 2.4 seconds 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 14 sheets defined 53.8% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 205 through 227 Proline residue: A 212 - end of helix removed outlier: 3.589A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 265 Processing helix chain 'A' and resid 278 through 303 Processing helix chain 'A' and resid 307 through 324 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 411 through 426 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 464 through 484 removed outlier: 3.584A pdb=" N HIS A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 227 Proline residue: B 212 - end of helix removed outlier: 3.588A pdb=" N ILE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 265 Processing helix chain 'B' and resid 278 through 303 Processing helix chain 'B' and resid 307 through 324 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 411 through 426 Proline residue: B 415 - end of helix Processing helix chain 'B' and resid 464 through 484 removed outlier: 3.585A pdb=" N HIS B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 227 Proline residue: C 212 - end of helix removed outlier: 3.588A pdb=" N ILE C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 265 Processing helix chain 'C' and resid 278 through 303 Processing helix chain 'C' and resid 307 through 324 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 411 through 426 Proline residue: C 415 - end of helix Processing helix chain 'C' and resid 464 through 484 removed outlier: 3.584A pdb=" N HIS C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 227 Proline residue: D 212 - end of helix removed outlier: 3.588A pdb=" N ILE D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 265 Processing helix chain 'D' and resid 278 through 303 Processing helix chain 'D' and resid 307 through 324 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 411 through 426 Proline residue: D 415 - end of helix Processing helix chain 'D' and resid 464 through 484 removed outlier: 3.584A pdb=" N HIS D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 227 Proline residue: E 212 - end of helix removed outlier: 3.588A pdb=" N ILE E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 265 Processing helix chain 'E' and resid 278 through 303 Processing helix chain 'E' and resid 307 through 324 Processing helix chain 'E' and resid 326 through 340 Processing helix chain 'E' and resid 381 through 383 No H-bonds generated for 'chain 'E' and resid 381 through 383' Processing helix chain 'E' and resid 411 through 426 Proline residue: E 415 - end of helix Processing helix chain 'E' and resid 464 through 484 removed outlier: 3.584A pdb=" N HIS E 484 " --> pdb=" O ILE E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Proline residue: F 212 - end of helix removed outlier: 3.588A pdb=" N ILE F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 265 Processing helix chain 'F' and resid 278 through 303 Processing helix chain 'F' and resid 307 through 324 Processing helix chain 'F' and resid 326 through 340 Processing helix chain 'F' and resid 381 through 383 No H-bonds generated for 'chain 'F' and resid 381 through 383' Processing helix chain 'F' and resid 411 through 426 Proline residue: F 415 - end of helix Processing helix chain 'F' and resid 464 through 484 removed outlier: 3.584A pdb=" N HIS F 484 " --> pdb=" O ILE F 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 227 Proline residue: G 212 - end of helix removed outlier: 3.588A pdb=" N ILE G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 265 Processing helix chain 'G' and resid 278 through 303 Processing helix chain 'G' and resid 307 through 324 Processing helix chain 'G' and resid 326 through 340 Processing helix chain 'G' and resid 381 through 383 No H-bonds generated for 'chain 'G' and resid 381 through 383' Processing helix chain 'G' and resid 411 through 426 Proline residue: G 415 - end of helix Processing helix chain 'G' and resid 464 through 484 removed outlier: 3.583A pdb=" N HIS G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 389 through 391 removed outlier: 6.470A pdb=" N SER A 368 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N MET A 362 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N THR A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 397 through 406 removed outlier: 3.800A pdb=" N ARG A 444 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR A 453 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU A 442 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY A 455 " --> pdb=" O CYS A 440 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N CYS A 440 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 389 through 391 removed outlier: 6.470A pdb=" N SER B 368 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N MET B 362 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N THR B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 397 through 406 removed outlier: 3.800A pdb=" N ARG B 444 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR B 453 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU B 442 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLY B 455 " --> pdb=" O CYS B 440 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N CYS B 440 " --> pdb=" O GLY B 455 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 389 through 391 removed outlier: 6.470A pdb=" N SER C 368 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N MET C 362 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR C 366 " --> pdb=" O MET C 362 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 397 through 406 removed outlier: 3.800A pdb=" N ARG C 444 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR C 453 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU C 442 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY C 455 " --> pdb=" O CYS C 440 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N CYS C 440 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 389 through 391 removed outlier: 6.471A pdb=" N SER D 368 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N MET D 362 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N THR D 366 " --> pdb=" O MET D 362 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 397 through 406 removed outlier: 3.800A pdb=" N ARG D 444 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR D 453 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU D 442 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY D 455 " --> pdb=" O CYS D 440 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N CYS D 440 " --> pdb=" O GLY D 455 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 389 through 391 removed outlier: 6.471A pdb=" N SER E 368 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N MET E 362 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N THR E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 397 through 406 removed outlier: 3.800A pdb=" N ARG E 444 " --> pdb=" O GLU E 451 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR E 453 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU E 442 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY E 455 " --> pdb=" O CYS E 440 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N CYS E 440 " --> pdb=" O GLY E 455 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 389 through 391 removed outlier: 6.470A pdb=" N SER F 368 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N MET F 362 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 397 through 406 removed outlier: 3.800A pdb=" N ARG F 444 " --> pdb=" O GLU F 451 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR F 453 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU F 442 " --> pdb=" O THR F 453 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY F 455 " --> pdb=" O CYS F 440 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N CYS F 440 " --> pdb=" O GLY F 455 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 389 through 391 removed outlier: 6.470A pdb=" N SER G 368 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N MET G 362 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR G 366 " --> pdb=" O MET G 362 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 397 through 406 removed outlier: 3.800A pdb=" N ARG G 444 " --> pdb=" O GLU G 451 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR G 453 " --> pdb=" O LEU G 442 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU G 442 " --> pdb=" O THR G 453 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY G 455 " --> pdb=" O CYS G 440 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N CYS G 440 " --> pdb=" O GLY G 455 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2625 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: 4.49 Time building geometry restraints manager: 6.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4300 1.33 - 1.45: 2268 1.45 - 1.57: 8559 1.57 - 1.69: 0 1.69 - 1.80: 147 Bond restraints: 15274 Sorted by residual: bond pdb=" C11 LFA E1102 " pdb=" C12 LFA E1102 " ideal model delta sigma weight residual 1.524 1.383 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C11 LFA B1101 " pdb=" C12 LFA B1101 " ideal model delta sigma weight residual 1.524 1.383 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C7 LFA D1101 " pdb=" C8 LFA D1101 " ideal model delta sigma weight residual 1.524 1.383 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C7 LFA A1101 " pdb=" C8 LFA A1101 " ideal model delta sigma weight residual 1.524 1.383 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C8 LFA G1103 " pdb=" C9 LFA G1103 " ideal model delta sigma weight residual 1.524 1.384 0.140 2.00e-02 2.50e+03 4.93e+01 ... (remaining 15269 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.40: 333 106.40 - 113.30: 8605 113.30 - 120.20: 5566 120.20 - 127.10: 5911 127.10 - 134.00: 123 Bond angle restraints: 20538 Sorted by residual: angle pdb=" N THR C 264 " pdb=" CA THR C 264 " pdb=" C THR C 264 " ideal model delta sigma weight residual 113.12 100.59 12.53 1.25e+00 6.40e-01 1.01e+02 angle pdb=" N THR G 264 " pdb=" CA THR G 264 " pdb=" C THR G 264 " ideal model delta sigma weight residual 113.12 100.59 12.53 1.25e+00 6.40e-01 1.00e+02 angle pdb=" N THR F 264 " pdb=" CA THR F 264 " pdb=" C THR F 264 " ideal model delta sigma weight residual 113.12 100.61 12.51 1.25e+00 6.40e-01 1.00e+02 angle pdb=" N THR E 264 " pdb=" CA THR E 264 " pdb=" C THR E 264 " ideal model delta sigma weight residual 113.12 100.61 12.51 1.25e+00 6.40e-01 1.00e+02 angle pdb=" N THR D 264 " pdb=" CA THR D 264 " pdb=" C THR D 264 " ideal model delta sigma weight residual 113.12 100.62 12.50 1.25e+00 6.40e-01 1.00e+02 ... (remaining 20533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.62: 8303 13.62 - 27.24: 637 27.24 - 40.86: 237 40.86 - 54.48: 42 54.48 - 68.10: 35 Dihedral angle restraints: 9254 sinusoidal: 3703 harmonic: 5551 Sorted by residual: dihedral pdb=" CA ASN G 261 " pdb=" CB ASN G 261 " pdb=" CG ASN G 261 " pdb=" OD1 ASN G 261 " ideal model delta sinusoidal sigma weight residual 120.00 -171.90 -68.10 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN F 261 " pdb=" CB ASN F 261 " pdb=" CG ASN F 261 " pdb=" OD1 ASN F 261 " ideal model delta sinusoidal sigma weight residual 120.00 -171.90 -68.10 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN D 261 " pdb=" CB ASN D 261 " pdb=" CG ASN D 261 " pdb=" OD1 ASN D 261 " ideal model delta sinusoidal sigma weight residual 120.00 -171.91 -68.09 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 9251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1791 0.051 - 0.103: 533 0.103 - 0.154: 102 0.154 - 0.206: 3 0.206 - 0.257: 14 Chirality restraints: 2443 Sorted by residual: chirality pdb=" CA MET C 266 " pdb=" N MET C 266 " pdb=" C MET C 266 " pdb=" CB MET C 266 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA MET B 266 " pdb=" N MET B 266 " pdb=" C MET B 266 " pdb=" CB MET B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA MET G 266 " pdb=" N MET G 266 " pdb=" C MET G 266 " pdb=" CB MET G 266 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2440 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 375 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO B 376 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 376 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 376 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 375 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO C 376 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 376 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 376 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 375 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO E 376 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 376 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 376 " 0.026 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1954 2.75 - 3.29: 14084 3.29 - 3.82: 23236 3.82 - 4.36: 28077 4.36 - 4.90: 50459 Nonbonded interactions: 117810 Sorted by model distance: nonbonded pdb=" OG SER G 443 " pdb=" OE1 GLU G 451 " model vdw 2.208 2.440 nonbonded pdb=" OG SER B 443 " pdb=" OE1 GLU B 451 " model vdw 2.209 2.440 nonbonded pdb=" OG SER F 443 " pdb=" OE1 GLU F 451 " model vdw 2.209 2.440 nonbonded pdb=" OG SER E 443 " pdb=" OE1 GLU E 451 " model vdw 2.209 2.440 nonbonded pdb=" OG SER A 443 " pdb=" OE1 GLU A 451 " model vdw 2.209 2.440 ... (remaining 117805 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9779 2.51 5 N 2485 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.940 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.140 Process input model: 41.310 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.018 0.141 15274 Z= 1.186 Angle : 1.016 12.532 20538 Z= 0.522 Chirality : 0.052 0.257 2443 Planarity : 0.005 0.047 2520 Dihedral : 12.836 68.101 5656 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.17), residues: 1897 helix: -0.02 (0.15), residues: 1092 sheet: -2.53 (0.24), residues: 280 loop : -3.35 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.964 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2262 time to fit residues: 64.1102 Evaluate side-chains 125 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 308 GLN A 331 ASN A 339 GLN A 387 GLN A 428 ASN B 261 ASN B 308 GLN B 331 ASN B 339 GLN B 387 GLN B 428 ASN C 308 GLN C 331 ASN C 339 GLN C 387 GLN C 428 ASN D 261 ASN D 308 GLN D 331 ASN D 339 GLN D 387 GLN D 428 ASN E 261 ASN E 308 GLN E 331 ASN E 339 GLN E 387 GLN E 428 ASN F 261 ASN F 308 GLN F 331 ASN F 339 GLN F 387 GLN F 428 ASN G 261 ASN G 308 GLN G 331 ASN G 339 GLN G 387 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 15274 Z= 0.165 Angle : 0.463 5.700 20538 Z= 0.234 Chirality : 0.039 0.153 2443 Planarity : 0.004 0.032 2520 Dihedral : 7.479 53.152 2212 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.05 % 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: -0.06 (0.20), residues: 1897 helix: 1.68 (0.16), residues: 1085 sheet: -1.95 (0.28), residues: 280 loop : -2.64 (0.21), residues: 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 148 average time/residue: 0.1953 time to fit residues: 47.7596 Evaluate side-chains 132 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1308 time to fit residues: 3.2864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 137 optimal weight: 0.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 GLN C 471 GLN D 471 GLN G 261 ASN G 471 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15274 Z= 0.150 Angle : 0.414 5.637 20538 Z= 0.211 Chirality : 0.038 0.156 2443 Planarity : 0.003 0.027 2520 Dihedral : 6.460 51.294 2212 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 1.24 % 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: 0.71 (0.20), residues: 1897 helix: 2.21 (0.17), residues: 1092 sheet: -1.69 (0.29), residues: 280 loop : -2.10 (0.22), residues: 525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 148 average time/residue: 0.1898 time to fit residues: 47.7331 Evaluate side-chains 144 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1136 time to fit residues: 4.8611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN G 428 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 15274 Z= 0.272 Angle : 0.466 5.892 20538 Z= 0.236 Chirality : 0.040 0.123 2443 Planarity : 0.003 0.030 2520 Dihedral : 6.373 57.143 2212 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.87 % 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: 0.75 (0.20), residues: 1897 helix: 2.12 (0.16), residues: 1141 sheet: -1.79 (0.28), residues: 273 loop : -2.10 (0.24), residues: 483 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 141 average time/residue: 0.1735 time to fit residues: 41.2754 Evaluate side-chains 140 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0989 time to fit residues: 3.2818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 0.0770 chunk 155 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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: 0.8174 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 15274 Z= 0.122 Angle : 0.396 5.599 20538 Z= 0.203 Chirality : 0.038 0.116 2443 Planarity : 0.003 0.024 2520 Dihedral : 5.813 59.693 2212 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.19 % 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: 1.39 (0.20), residues: 1897 helix: 2.68 (0.16), residues: 1092 sheet: -1.35 (0.29), residues: 280 loop : -1.66 (0.24), residues: 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 137 average time/residue: 0.1742 time to fit residues: 40.6242 Evaluate side-chains 137 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1573 time to fit residues: 2.9328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 57.3817 > 50: distance: 127 - 219: 12.253 distance: 130 - 216: 12.295 distance: 139 - 204: 34.085 distance: 142 - 201: 20.957 distance: 167 - 174: 18.518 distance: 174 - 175: 23.936 distance: 175 - 176: 20.810 distance: 175 - 178: 14.033 distance: 176 - 177: 35.247 distance: 176 - 183: 14.161 distance: 178 - 179: 14.040 distance: 179 - 180: 14.480 distance: 180 - 181: 13.939 distance: 181 - 182: 8.436 distance: 183 - 184: 21.495 distance: 184 - 185: 18.828 distance: 184 - 187: 40.666 distance: 185 - 186: 5.010 distance: 185 - 194: 8.822 distance: 187 - 188: 5.083 distance: 188 - 189: 25.205 distance: 188 - 190: 5.444 distance: 189 - 191: 12.421 distance: 190 - 192: 15.606 distance: 191 - 193: 11.886 distance: 192 - 193: 24.361 distance: 194 - 195: 11.224 distance: 194 - 200: 34.843 distance: 195 - 196: 29.275 distance: 195 - 198: 30.076 distance: 196 - 197: 4.465 distance: 196 - 201: 15.579 distance: 198 - 199: 9.533 distance: 199 - 200: 15.915 distance: 201 - 202: 15.313 distance: 202 - 205: 19.998 distance: 203 - 204: 44.857 distance: 203 - 208: 12.160 distance: 205 - 206: 38.309 distance: 205 - 207: 25.366 distance: 208 - 209: 19.382 distance: 209 - 210: 9.518 distance: 209 - 212: 27.839 distance: 210 - 211: 24.333 distance: 210 - 216: 5.981 distance: 212 - 213: 12.980 distance: 213 - 214: 9.155 distance: 213 - 215: 9.579 distance: 216 - 217: 15.971 distance: 217 - 218: 12.969 distance: 217 - 220: 18.567 distance: 218 - 219: 4.326 distance: 218 - 223: 8.758 distance: 220 - 221: 5.896 distance: 220 - 222: 9.334 distance: 223 - 224: 6.359 distance: 223 - 229: 3.238 distance: 224 - 225: 4.799 distance: 224 - 227: 5.923 distance: 225 - 226: 6.642 distance: 225 - 230: 8.747 distance: 227 - 228: 9.377 distance: 228 - 229: 5.352 distance: 230 - 231: 12.231 distance: 231 - 232: 10.029 distance: 231 - 234: 3.947 distance: 232 - 233: 11.178 distance: 232 - 238: 14.258 distance: 234 - 235: 23.469 distance: 235 - 236: 8.755 distance: 235 - 237: 18.014 distance: 238 - 239: 23.280 distance: 239 - 240: 13.987 distance: 239 - 242: 27.680 distance: 240 - 241: 18.135 distance: 240 - 244: 21.432 distance: 242 - 243: 17.213 distance: 244 - 245: 13.550 distance: 245 - 246: 18.379 distance: 245 - 248: 11.681 distance: 246 - 247: 19.294 distance: 246 - 252: 13.349 distance: 248 - 249: 19.299 distance: 249 - 250: 23.883 distance: 249 - 251: 18.344