Starting phenix.real_space_refine on Fri Feb 16 10:26:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/02_2024/6vxm_21444_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/02_2024/6vxm_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_21444/02_2024/6vxm_21444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/02_2024/6vxm_21444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/02_2024/6vxm_21444_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/02_2024/6vxm_21444_updated.pdb" } resolution = 3.06 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= 0.000 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 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. 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-5238/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: 8.08, per 1000 atoms: 0.54 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: 5.82 Conformation dependent library (CDL) restraints added in 3.1 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: 3.01 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: 4.81 Time building geometry restraints manager: 6.32 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 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: 0.820 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: 4.310 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 42.760 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 % Allowed : 6.93 % Favored : 93.07 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 397 HIS 0.005 0.002 HIS E 439 PHE 0.010 0.002 PHE C 340 TYR 0.011 0.002 TYR E 441 ARG 0.004 0.001 ARG C 444 *********************** 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 : 1.870 Fit side-chains REVERT: B 215 TYR cc_start: 0.7145 (m-80) cc_final: 0.6755 (m-80) REVERT: C 215 TYR cc_start: 0.7050 (m-80) cc_final: 0.6739 (m-80) REVERT: C 410 ASP cc_start: 0.7046 (t0) cc_final: 0.6603 (t0) REVERT: D 410 ASP cc_start: 0.7084 (t0) cc_final: 0.6881 (t0) REVERT: E 410 ASP cc_start: 0.7095 (t0) cc_final: 0.6632 (t0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2332 time to fit residues: 65.8941 Evaluate side-chains 125 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 G 261 ASN G 308 GLN G 331 ASN G 339 GLN G 387 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15274 Z= 0.164 Angle : 0.463 5.701 20538 Z= 0.234 Chirality : 0.039 0.154 2443 Planarity : 0.004 0.033 2520 Dihedral : 7.516 53.358 2212 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.05 % Allowed : 9.34 % Favored : 89.61 % 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: -0.13 (0.20), residues: 1897 helix: 1.60 (0.16), residues: 1092 sheet: -1.97 (0.28), residues: 280 loop : -2.65 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 253 HIS 0.001 0.001 HIS A 484 PHE 0.006 0.001 PHE B 323 TYR 0.005 0.000 TYR A 467 ARG 0.002 0.000 ARG F 265 *********************** 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 : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 461 MET cc_start: 0.7881 (ptp) cc_final: 0.7650 (ptm) outliers start: 17 outliers final: 5 residues processed: 148 average time/residue: 0.2035 time to fit residues: 50.6301 Evaluate side-chains 132 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 F 428 ASN G 261 ASN G 471 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15274 Z= 0.143 Angle : 0.411 5.626 20538 Z= 0.210 Chirality : 0.038 0.158 2443 Planarity : 0.003 0.027 2520 Dihedral : 6.510 51.853 2212 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.48 % Allowed : 10.58 % Favored : 87.94 % 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: 0.69 (0.20), residues: 1897 helix: 2.19 (0.17), residues: 1092 sheet: -1.70 (0.29), residues: 280 loop : -2.11 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 253 HIS 0.001 0.000 HIS A 484 PHE 0.006 0.001 PHE F 323 TYR 0.002 0.000 TYR D 441 ARG 0.001 0.000 ARG C 398 *********************** 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 158 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: D 215 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.6231 (m-80) REVERT: D 410 ASP cc_start: 0.6987 (t0) cc_final: 0.6080 (t0) REVERT: E 215 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6562 (m-80) REVERT: F 215 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: F 461 MET cc_start: 0.7953 (ptp) cc_final: 0.7513 (ptp) outliers start: 24 outliers final: 15 residues processed: 148 average time/residue: 0.1903 time to fit residues: 48.1868 Evaluate side-chains 151 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.8035 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15274 Z= 0.289 Angle : 0.470 6.031 20538 Z= 0.238 Chirality : 0.040 0.122 2443 Planarity : 0.003 0.031 2520 Dihedral : 6.420 55.178 2212 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.23 % Allowed : 10.02 % Favored : 87.76 % 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: 0.72 (0.20), residues: 1897 helix: 2.10 (0.16), residues: 1141 sheet: -1.80 (0.28), residues: 273 loop : -2.15 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 253 HIS 0.001 0.000 HIS G 484 PHE 0.010 0.001 PHE A 323 TYR 0.004 0.001 TYR G 256 ARG 0.001 0.000 ARG A 398 *********************** 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 168 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6444 (m-80) REVERT: A 311 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8268 (mp) REVERT: B 215 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6761 (m-80) REVERT: D 215 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6482 (m-80) REVERT: E 215 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6648 (m-80) REVERT: F 215 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: F 461 MET cc_start: 0.7934 (ptp) cc_final: 0.7533 (ptp) outliers start: 36 outliers final: 24 residues processed: 152 average time/residue: 0.1959 time to fit residues: 51.0711 Evaluate side-chains 162 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 2 optimal weight: 0.0870 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 0.0670 chunk 155 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.1898 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15274 Z= 0.164 Angle : 0.411 5.610 20538 Z= 0.210 Chirality : 0.038 0.122 2443 Planarity : 0.003 0.027 2520 Dihedral : 6.079 59.691 2212 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.48 % Allowed : 11.94 % Favored : 86.58 % 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: 1.33 (0.20), residues: 1897 helix: 2.59 (0.17), residues: 1099 sheet: -1.34 (0.30), residues: 280 loop : -1.66 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 253 HIS 0.001 0.000 HIS G 484 PHE 0.006 0.001 PHE A 323 TYR 0.002 0.000 TYR E 256 ARG 0.001 0.000 ARG F 277 *********************** 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 159 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.6376 (m-80) REVERT: A 305 VAL cc_start: 0.8811 (m) cc_final: 0.8609 (m) REVERT: A 311 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8162 (mp) REVERT: B 215 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: D 215 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: D 228 MET cc_start: 0.8053 (ttm) cc_final: 0.7779 (ttt) REVERT: E 215 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6650 (m-80) REVERT: F 215 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6307 (m-80) REVERT: F 461 MET cc_start: 0.7870 (ptp) cc_final: 0.7496 (ptp) outliers start: 24 outliers final: 17 residues processed: 148 average time/residue: 0.1868 time to fit residues: 47.4738 Evaluate side-chains 157 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.0170 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15274 Z= 0.207 Angle : 0.424 5.875 20538 Z= 0.216 Chirality : 0.039 0.119 2443 Planarity : 0.003 0.025 2520 Dihedral : 6.035 59.845 2212 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.54 % Allowed : 11.56 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.20), residues: 1897 helix: 2.71 (0.16), residues: 1099 sheet: -1.16 (0.30), residues: 280 loop : -1.57 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 253 HIS 0.001 0.000 HIS G 484 PHE 0.008 0.001 PHE A 323 TYR 0.003 0.000 TYR G 256 ARG 0.001 0.000 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 6 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 175 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.6445 (m-80) REVERT: A 267 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8569 (tt) REVERT: A 311 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8203 (mp) REVERT: B 215 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6779 (m-80) REVERT: B 267 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8472 (tt) REVERT: D 215 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: E 215 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6629 (m-80) REVERT: F 215 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6327 (m-80) REVERT: F 249 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8345 (mm) outliers start: 41 outliers final: 23 residues processed: 158 average time/residue: 0.1950 time to fit residues: 52.6756 Evaluate side-chains 166 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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: 0.7983 moved from start: 0.2414 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= 0.121 Angle : 0.400 6.641 20538 Z= 0.202 Chirality : 0.038 0.124 2443 Planarity : 0.003 0.024 2520 Dihedral : 5.580 59.341 2212 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.24 % Allowed : 12.68 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 1897 helix: 2.87 (0.16), residues: 1092 sheet: -1.03 (0.31), residues: 280 loop : -1.48 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 253 HIS 0.000 0.000 HIS E 439 PHE 0.005 0.001 PHE E 449 TYR 0.002 0.000 TYR E 256 ARG 0.001 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 7 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 156 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: B 215 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: D 215 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6445 (m-80) REVERT: D 410 ASP cc_start: 0.7128 (t0) cc_final: 0.6762 (t0) REVERT: E 215 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: F 215 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6307 (m-80) outliers start: 20 outliers final: 12 residues processed: 149 average time/residue: 0.1925 time to fit residues: 49.1638 Evaluate side-chains 153 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 143 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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: 0.7981 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15274 Z= 0.127 Angle : 0.397 5.725 20538 Z= 0.200 Chirality : 0.038 0.119 2443 Planarity : 0.003 0.025 2520 Dihedral : 5.260 54.635 2212 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.11 % Allowed : 12.99 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1897 helix: 2.92 (0.16), residues: 1099 sheet: -0.88 (0.31), residues: 280 loop : -1.34 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 253 HIS 0.000 0.000 HIS E 439 PHE 0.005 0.001 PHE A 323 TYR 0.002 0.000 TYR F 467 ARG 0.001 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 8 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 156 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: A 267 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8530 (tt) REVERT: B 215 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: B 267 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8422 (tt) REVERT: D 215 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6490 (m-80) REVERT: E 215 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6638 (m-80) REVERT: F 215 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6269 (m-80) outliers start: 18 outliers final: 11 residues processed: 149 average time/residue: 0.2225 time to fit residues: 56.9425 Evaluate side-chains 154 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15274 Z= 0.177 Angle : 0.413 5.558 20538 Z= 0.209 Chirality : 0.038 0.119 2443 Planarity : 0.003 0.026 2520 Dihedral : 5.287 53.950 2212 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.36 % Allowed : 12.93 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.21), residues: 1897 helix: 2.97 (0.16), residues: 1099 sheet: -0.83 (0.31), residues: 280 loop : -1.33 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 253 HIS 0.001 0.000 HIS E 484 PHE 0.006 0.001 PHE A 323 TYR 0.003 0.000 TYR C 256 ARG 0.001 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 9 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 159 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: A 267 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8554 (tt) REVERT: B 215 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6760 (m-80) REVERT: B 267 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8551 (tt) REVERT: D 215 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6536 (m-80) REVERT: E 215 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: F 215 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6284 (m-80) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 0.1918 time to fit residues: 49.7781 Evaluate side-chains 156 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 15 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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: 0.7994 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15274 Z= 0.149 Angle : 0.401 5.549 20538 Z= 0.204 Chirality : 0.038 0.118 2443 Planarity : 0.003 0.024 2520 Dihedral : 5.025 48.935 2212 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.18 % Allowed : 13.23 % Favored : 85.59 % 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: 1.99 (0.21), residues: 1897 helix: 3.01 (0.16), residues: 1099 sheet: -0.77 (0.31), residues: 280 loop : -1.31 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 253 HIS 0.000 0.000 HIS G 484 PHE 0.006 0.001 PHE C 323 TYR 0.002 0.000 TYR C 256 ARG 0.000 0.000 ARG E 277 ********************** REFINEMENT MACRO_CYCLE 10 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: 19 poor density : 136 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6504 (m-80) REVERT: A 267 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 215 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: B 267 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8538 (tt) REVERT: D 215 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: E 215 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6653 (m-80) REVERT: F 215 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6281 (m-80) outliers start: 19 outliers final: 12 residues processed: 149 average time/residue: 0.1858 time to fit residues: 47.4695 Evaluate side-chains 154 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 150 optimal weight: 0.0670 chunk 62 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 27 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.087924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.064431 restraints weight = 32385.731| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.24 r_work: 0.2706 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15274 Z= 0.195 Angle : 0.420 5.566 20538 Z= 0.213 Chirality : 0.038 0.119 2443 Planarity : 0.003 0.025 2520 Dihedral : 5.172 52.109 2212 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.24 % Allowed : 13.05 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.21), residues: 1897 helix: 3.05 (0.16), residues: 1099 sheet: -0.75 (0.31), residues: 280 loop : -1.34 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 253 HIS 0.001 0.000 HIS G 484 PHE 0.007 0.001 PHE A 323 TYR 0.003 0.000 TYR C 256 ARG 0.001 0.000 ARG B 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2598.91 seconds wall clock time: 48 minutes 43.63 seconds (2923.63 seconds total)