Starting phenix.real_space_refine on Fri Feb 16 04:42:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/02_2024/6vxn_21445_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/02_2024/6vxn_21445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/02_2024/6vxn_21445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/02_2024/6vxn_21445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/02_2024/6vxn_21445_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/02_2024/6vxn_21445_updated.pdb" } resolution = 2.96 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= 0.003 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 77 5.16 5 C 9296 2.51 5 N 2394 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 326": "NH1" <-> "NH2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D GLU 356": "OE1" <-> "OE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D ARG 444": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "E ARG 326": "NH1" <-> "NH2" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E GLU 423": "OE1" <-> "OE2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "E ARG 460": "NH1" <-> "NH2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F GLU 423": "OE1" <-> "OE2" Residue "F ARG 426": "NH1" <-> "NH2" Residue "F ARG 444": "NH1" <-> "NH2" Residue "F ARG 460": "NH1" <-> "NH2" Residue "F GLU 476": "OE1" <-> "OE2" Residue "G ARG 265": "NH1" <-> "NH2" Residue "G ARG 326": "NH1" <-> "NH2" Residue "G GLU 356": "OE1" <-> "OE2" Residue "G GLU 423": "OE1" <-> "OE2" Residue "G ARG 426": "NH1" <-> "NH2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "G ARG 460": "NH1" <-> "NH2" Residue "G GLU 476": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14385 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "B" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "C" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "D" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "E" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "F" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "G" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'D12': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'D12': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'D12': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'D12': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'D12': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.08, per 1000 atoms: 0.56 Number of scatterers: 14385 At special positions: 0 Unit cell: (121, 119.9, 101.2, 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 77 16.00 O 2618 8.00 N 2394 7.00 C 9296 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: 4.99 Conformation dependent library (CDL) restraints added in 2.5 seconds 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3458 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 14 sheets defined 53.4% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 205 through 226 Proline residue: A 212 - end of helix removed outlier: 3.760A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 268 Processing helix chain 'A' and resid 278 through 299 Processing helix chain 'A' and resid 316 through 340 removed outlier: 3.632A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 411 through 427 Proline residue: A 415 - end of helix removed outlier: 4.074A pdb=" N SER A 427 " --> pdb=" O MET A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 484 removed outlier: 3.837A pdb=" N TYR A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 226 Proline residue: B 212 - end of helix removed outlier: 3.761A pdb=" N ILE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 268 Processing helix chain 'B' and resid 278 through 299 Processing helix chain 'B' and resid 316 through 340 removed outlier: 3.632A pdb=" N GLN B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 384 Processing helix chain 'B' and resid 411 through 427 Proline residue: B 415 - end of helix removed outlier: 4.074A pdb=" N SER B 427 " --> pdb=" O MET B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 484 removed outlier: 3.837A pdb=" N TYR B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 226 Proline residue: C 212 - end of helix removed outlier: 3.760A pdb=" N ILE C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 268 Processing helix chain 'C' and resid 278 through 299 Processing helix chain 'C' and resid 316 through 340 removed outlier: 3.631A pdb=" N GLN C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 384 Processing helix chain 'C' and resid 411 through 427 Proline residue: C 415 - end of helix removed outlier: 4.074A pdb=" N SER C 427 " --> pdb=" O MET C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 484 removed outlier: 3.837A pdb=" N TYR C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 226 Proline residue: D 212 - end of helix removed outlier: 3.760A pdb=" N ILE D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 268 Processing helix chain 'D' and resid 278 through 299 Processing helix chain 'D' and resid 316 through 340 removed outlier: 3.631A pdb=" N GLN D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 384 Processing helix chain 'D' and resid 411 through 427 Proline residue: D 415 - end of helix removed outlier: 4.074A pdb=" N SER D 427 " --> pdb=" O MET D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 484 removed outlier: 3.837A pdb=" N TYR D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 226 Proline residue: E 212 - end of helix removed outlier: 3.760A pdb=" N ILE E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 268 Processing helix chain 'E' and resid 278 through 299 Processing helix chain 'E' and resid 316 through 340 removed outlier: 3.631A pdb=" N GLN E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 384 Processing helix chain 'E' and resid 411 through 427 Proline residue: E 415 - end of helix removed outlier: 4.074A pdb=" N SER E 427 " --> pdb=" O MET E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 484 removed outlier: 3.837A pdb=" N TYR E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS E 484 " --> pdb=" O ILE E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 226 Proline residue: F 212 - end of helix removed outlier: 3.760A pdb=" N ILE F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 268 Processing helix chain 'F' and resid 278 through 299 Processing helix chain 'F' and resid 316 through 340 removed outlier: 3.632A pdb=" N GLN F 339 " --> pdb=" O GLY F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 384 Processing helix chain 'F' and resid 411 through 427 Proline residue: F 415 - end of helix removed outlier: 4.074A pdb=" N SER F 427 " --> pdb=" O MET F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 484 removed outlier: 3.838A pdb=" N TYR F 467 " --> pdb=" O LYS F 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS F 484 " --> pdb=" O ILE F 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 226 Proline residue: G 212 - end of helix removed outlier: 3.760A pdb=" N ILE G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 268 Processing helix chain 'G' and resid 278 through 299 Processing helix chain 'G' and resid 316 through 340 removed outlier: 3.631A pdb=" N GLN G 339 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 384 Processing helix chain 'G' and resid 411 through 427 Proline residue: G 415 - end of helix removed outlier: 4.075A pdb=" N SER G 427 " --> pdb=" O MET G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 484 removed outlier: 3.837A pdb=" N TYR G 467 " --> pdb=" O LYS G 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.533A pdb=" N VAL A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER A 368 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N MET A 362 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.321A 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: 4.056A pdb=" N ARG A 444 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR A 453 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU A 442 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY A 455 " --> pdb=" O CYS A 440 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N CYS A 440 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 349 through 352 removed outlier: 3.534A pdb=" N VAL B 355 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER B 368 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N MET B 362 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 7.321A 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: 4.056A pdb=" N ARG B 444 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR B 453 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU B 442 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY B 455 " --> pdb=" O CYS B 440 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N CYS B 440 " --> pdb=" O GLY B 455 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 349 through 352 removed outlier: 3.533A pdb=" N VAL C 355 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER C 368 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N MET C 362 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 7.320A 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: 4.057A pdb=" N ARG C 444 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 453 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU C 442 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY C 455 " --> pdb=" O CYS C 440 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N CYS C 440 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 349 through 352 removed outlier: 3.533A pdb=" N VAL D 355 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER D 368 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N MET D 362 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 7.320A 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: 4.056A pdb=" N ARG D 444 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR D 453 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU D 442 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY D 455 " --> pdb=" O CYS D 440 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N CYS D 440 " --> pdb=" O GLY D 455 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 349 through 352 removed outlier: 3.533A pdb=" N VAL E 355 " --> pdb=" O ALA E 352 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER E 368 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N MET E 362 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 7.320A 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: 4.056A pdb=" N ARG E 444 " --> pdb=" O GLU E 451 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR E 453 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU E 442 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY E 455 " --> pdb=" O CYS E 440 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N CYS E 440 " --> pdb=" O GLY E 455 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 349 through 352 removed outlier: 3.533A pdb=" N VAL F 355 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER F 368 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N MET F 362 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 7.320A 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: 4.056A pdb=" N ARG F 444 " --> pdb=" O GLU F 451 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR F 453 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU F 442 " --> pdb=" O THR F 453 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY F 455 " --> pdb=" O CYS F 440 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N CYS F 440 " --> pdb=" O GLY F 455 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 349 through 352 removed outlier: 3.533A pdb=" N VAL G 355 " --> pdb=" O ALA G 352 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER G 368 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N MET G 362 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 7.320A 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: 4.056A pdb=" N ARG G 444 " --> pdb=" O GLU G 451 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR G 453 " --> pdb=" O LEU G 442 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU G 442 " --> pdb=" O THR G 453 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY G 455 " --> pdb=" O CYS G 440 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N CYS G 440 " --> pdb=" O GLY G 455 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2436 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: 4.34 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4413 1.34 - 1.46: 3168 1.46 - 1.58: 6881 1.58 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 14602 Sorted by residual: bond pdb=" C PRO C 343 " pdb=" N PHE C 344 " ideal model delta sigma weight residual 1.330 1.462 -0.132 1.26e-02 6.30e+03 1.10e+02 bond pdb=" C PRO D 343 " pdb=" N PHE D 344 " ideal model delta sigma weight residual 1.330 1.462 -0.132 1.26e-02 6.30e+03 1.10e+02 bond pdb=" C PRO A 343 " pdb=" N PHE A 344 " ideal model delta sigma weight residual 1.330 1.462 -0.132 1.26e-02 6.30e+03 1.09e+02 bond pdb=" C PRO F 343 " pdb=" N PHE F 344 " ideal model delta sigma weight residual 1.330 1.462 -0.131 1.26e-02 6.30e+03 1.09e+02 bond pdb=" C PRO G 343 " pdb=" N PHE G 344 " ideal model delta sigma weight residual 1.330 1.461 -0.131 1.26e-02 6.30e+03 1.08e+02 ... (remaining 14597 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.98: 343 106.98 - 113.82: 8441 113.82 - 120.65: 6167 120.65 - 127.49: 4614 127.49 - 134.32: 119 Bond angle restraints: 19684 Sorted by residual: angle pdb=" C MET E 413 " pdb=" N ILE E 414 " pdb=" CA ILE E 414 " ideal model delta sigma weight residual 120.24 124.10 -3.86 6.30e-01 2.52e+00 3.75e+01 angle pdb=" C MET B 413 " pdb=" N ILE B 414 " pdb=" CA ILE B 414 " ideal model delta sigma weight residual 120.24 124.09 -3.85 6.30e-01 2.52e+00 3.74e+01 angle pdb=" C MET G 413 " pdb=" N ILE G 414 " pdb=" CA ILE G 414 " ideal model delta sigma weight residual 120.24 124.08 -3.84 6.30e-01 2.52e+00 3.71e+01 angle pdb=" C MET C 413 " pdb=" N ILE C 414 " pdb=" CA ILE C 414 " ideal model delta sigma weight residual 120.24 124.07 -3.83 6.30e-01 2.52e+00 3.70e+01 angle pdb=" C MET A 413 " pdb=" N ILE A 414 " pdb=" CA ILE A 414 " ideal model delta sigma weight residual 120.24 124.06 -3.82 6.30e-01 2.52e+00 3.67e+01 ... (remaining 19679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 7601 14.82 - 29.65: 757 29.65 - 44.47: 280 44.47 - 59.29: 126 59.29 - 74.11: 42 Dihedral angle restraints: 8806 sinusoidal: 3479 harmonic: 5327 Sorted by residual: dihedral pdb=" CA MET C 297 " pdb=" C MET C 297 " pdb=" N ALA C 298 " pdb=" CA ALA C 298 " ideal model delta harmonic sigma weight residual 180.00 164.03 15.97 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA MET F 297 " pdb=" C MET F 297 " pdb=" N ALA F 298 " pdb=" CA ALA F 298 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA MET B 297 " pdb=" C MET B 297 " pdb=" N ALA B 298 " pdb=" CA ALA B 298 " ideal model delta harmonic sigma weight residual 180.00 164.05 15.95 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 8803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1958 0.074 - 0.147: 332 0.147 - 0.221: 48 0.221 - 0.294: 0 0.294 - 0.368: 7 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CB ILE D 263 " pdb=" CA ILE D 263 " pdb=" CG1 ILE D 263 " pdb=" CG2 ILE D 263 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CB ILE B 263 " pdb=" CA ILE B 263 " pdb=" CG1 ILE B 263 " pdb=" CG2 ILE B 263 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB ILE A 263 " pdb=" CA ILE A 263 " pdb=" CG1 ILE A 263 " pdb=" CG2 ILE A 263 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 2342 not shown) Planarity restraints: 2429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 421 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.64e+00 pdb=" C ILE D 421 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE D 421 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS D 422 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 421 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ILE B 421 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE B 421 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS B 422 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 421 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C ILE C 421 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE C 421 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS C 422 " -0.014 2.00e-02 2.50e+03 ... (remaining 2426 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4515 2.85 - 3.36: 12978 3.36 - 3.87: 22711 3.87 - 4.39: 25563 4.39 - 4.90: 44682 Nonbonded interactions: 110449 Sorted by model distance: nonbonded pdb=" O GLU D 465 " pdb=" OG1 THR D 469 " model vdw 2.332 2.440 nonbonded pdb=" O GLU A 465 " pdb=" OG1 THR A 469 " model vdw 2.333 2.440 nonbonded pdb=" O GLU F 465 " pdb=" OG1 THR F 469 " model vdw 2.333 2.440 nonbonded pdb=" O GLU G 465 " pdb=" OG1 THR G 469 " model vdw 2.333 2.440 nonbonded pdb=" O GLU E 465 " pdb=" OG1 THR E 469 " model vdw 2.333 2.440 ... (remaining 110444 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' and resid 204 through 491) selection = (chain 'C' and resid 204 through 491) selection = (chain 'D' and resid 204 through 491) selection = chain 'E' selection = (chain 'F' and resid 204 through 491) selection = (chain 'G' and resid 204 through 491) } 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: 1.080 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: 4.320 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 39.760 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.013 0.149 14602 Z= 0.845 Angle : 1.068 10.694 19684 Z= 0.572 Chirality : 0.062 0.368 2345 Planarity : 0.007 0.042 2429 Dihedral : 15.677 74.113 5348 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % 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: -3.41 (0.16), residues: 1806 helix: -1.92 (0.13), residues: 1015 sheet: -2.20 (0.23), residues: 364 loop : -2.41 (0.23), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP G 206 HIS 0.003 0.001 HIS C 439 PHE 0.017 0.002 PHE E 384 TYR 0.012 0.002 TYR F 441 ARG 0.007 0.001 ARG G 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.0446 (m100) cc_final: -0.0181 (m-90) REVERT: A 258 TRP cc_start: 0.8423 (t60) cc_final: 0.8146 (t60) REVERT: A 292 PHE cc_start: 0.7860 (t80) cc_final: 0.7403 (t80) REVERT: B 228 MET cc_start: 0.6865 (tpp) cc_final: 0.6629 (mmp) REVERT: B 292 PHE cc_start: 0.7815 (t80) cc_final: 0.7494 (t80) REVERT: B 323 PHE cc_start: 0.8960 (m-10) cc_final: 0.8735 (m-80) REVERT: C 258 TRP cc_start: 0.7993 (t60) cc_final: 0.7742 (t60) REVERT: C 261 ASN cc_start: 0.8834 (m110) cc_final: 0.8552 (m110) REVERT: C 292 PHE cc_start: 0.7909 (t80) cc_final: 0.7705 (t80) REVERT: C 339 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8469 (mm-40) REVERT: D 214 ARG cc_start: 0.5990 (ptt90) cc_final: 0.5441 (ptm-80) REVERT: D 224 GLN cc_start: 0.7509 (tt0) cc_final: 0.7235 (tp-100) REVERT: D 323 PHE cc_start: 0.8834 (m-10) cc_final: 0.8158 (m-80) REVERT: E 339 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8454 (mm-40) REVERT: F 292 PHE cc_start: 0.8070 (t80) cc_final: 0.7856 (t80) REVERT: G 258 TRP cc_start: 0.8106 (t60) cc_final: 0.7888 (t60) REVERT: G 292 PHE cc_start: 0.7939 (t80) cc_final: 0.7519 (OUTLIER) outliers start: 0 outliers final: 5 residues processed: 310 average time/residue: 1.3554 time to fit residues: 455.6205 Evaluate side-chains 192 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 410 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN A 457 ASN B 407 GLN B 457 ASN C 381 ASN C 416 GLN C 457 ASN D 457 ASN E 457 ASN F 381 ASN F 457 ASN G 457 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14602 Z= 0.184 Angle : 0.629 8.700 19684 Z= 0.314 Chirality : 0.042 0.221 2345 Planarity : 0.005 0.035 2429 Dihedral : 7.923 117.633 2017 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.67 % Allowed : 21.59 % Favored : 76.75 % 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: -1.41 (0.18), residues: 1806 helix: -0.16 (0.16), residues: 1008 sheet: -1.59 (0.25), residues: 350 loop : -1.79 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 206 HIS 0.001 0.000 HIS D 439 PHE 0.017 0.001 PHE F 323 TYR 0.017 0.001 TYR F 256 ARG 0.011 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.0138 (m100) cc_final: -0.0235 (p90) REVERT: A 258 TRP cc_start: 0.8276 (t60) cc_final: 0.8029 (t60) REVERT: A 266 MET cc_start: 0.7100 (ppp) cc_final: 0.6745 (mmt) REVERT: C 254 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8325 (t80) REVERT: C 292 PHE cc_start: 0.7894 (t80) cc_final: 0.7692 (t80) REVERT: D 228 MET cc_start: 0.4995 (mmp) cc_final: 0.4535 (mmp) REVERT: D 266 MET cc_start: 0.7417 (tmm) cc_final: 0.7006 (mmt) REVERT: D 319 VAL cc_start: 0.8748 (t) cc_final: 0.8291 (m) REVERT: D 323 PHE cc_start: 0.8828 (m-10) cc_final: 0.8609 (m-80) REVERT: E 224 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7327 (tt0) REVERT: E 339 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8505 (mm-40) REVERT: F 266 MET cc_start: 0.6885 (pp-130) cc_final: 0.6629 (mmt) REVERT: F 292 PHE cc_start: 0.7935 (t80) cc_final: 0.7682 (t80) REVERT: F 482 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8195 (mttm) REVERT: G 266 MET cc_start: 0.6993 (ppp) cc_final: 0.6358 (mmt) REVERT: G 292 PHE cc_start: 0.7872 (t80) cc_final: 0.7452 (t80) outliers start: 26 outliers final: 9 residues processed: 218 average time/residue: 1.0769 time to fit residues: 261.4983 Evaluate side-chains 195 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 416 GLN Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 112 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 132 optimal weight: 0.0370 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN C 396 GLN C 419 ASN G 358 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14602 Z= 0.294 Angle : 0.633 8.944 19684 Z= 0.315 Chirality : 0.043 0.219 2345 Planarity : 0.004 0.048 2429 Dihedral : 6.496 52.521 2009 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.18 % Allowed : 23.51 % Favored : 74.31 % 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: -0.43 (0.19), residues: 1806 helix: 0.70 (0.17), residues: 1001 sheet: -1.37 (0.28), residues: 315 loop : -1.38 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 206 HIS 0.003 0.001 HIS G 439 PHE 0.016 0.001 PHE G 254 TYR 0.015 0.001 TYR C 256 ARG 0.005 0.000 ARG F 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.0114 (m100) cc_final: -0.0293 (p90) REVERT: A 258 TRP cc_start: 0.8381 (t60) cc_final: 0.8086 (t60) REVERT: A 266 MET cc_start: 0.7096 (ppp) cc_final: 0.6777 (mmt) REVERT: C 254 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8388 (t80) REVERT: C 278 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: C 292 PHE cc_start: 0.7903 (t80) cc_final: 0.7656 (t80) REVERT: D 228 MET cc_start: 0.5322 (mmp) cc_final: 0.4915 (mmp) REVERT: D 266 MET cc_start: 0.7531 (tmm) cc_final: 0.7119 (ttt) REVERT: D 319 VAL cc_start: 0.8678 (t) cc_final: 0.8166 (m) REVERT: D 323 PHE cc_start: 0.8842 (m-10) cc_final: 0.8583 (m-80) REVERT: E 258 TRP cc_start: 0.8116 (OUTLIER) cc_final: 0.7443 (t-100) REVERT: E 261 ASN cc_start: 0.8362 (m110) cc_final: 0.7807 (m110) REVERT: E 339 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8533 (mm-40) REVERT: F 292 PHE cc_start: 0.8012 (t80) cc_final: 0.7746 (t80) REVERT: G 266 MET cc_start: 0.6922 (ppp) cc_final: 0.6474 (mmt) REVERT: G 292 PHE cc_start: 0.7873 (t80) cc_final: 0.7448 (t80) outliers start: 34 outliers final: 15 residues processed: 204 average time/residue: 1.0883 time to fit residues: 246.8813 Evaluate side-chains 191 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 416 GLN Chi-restraints excluded: chain E residue 258 TRP Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 346 MET Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 387 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 407 GLN B 419 ASN C 407 GLN D 407 GLN E 407 GLN E 419 ASN G 470 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14602 Z= 0.169 Angle : 0.591 9.248 19684 Z= 0.292 Chirality : 0.041 0.241 2345 Planarity : 0.003 0.031 2429 Dihedral : 5.932 50.747 2009 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.05 % Allowed : 24.34 % Favored : 73.61 % 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: 0.00 (0.20), residues: 1806 helix: 1.03 (0.17), residues: 994 sheet: -1.28 (0.29), residues: 315 loop : -1.05 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 206 HIS 0.000 0.000 HIS G 439 PHE 0.018 0.001 PHE G 254 TYR 0.012 0.000 TYR E 256 ARG 0.006 0.000 ARG E 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 206 TRP cc_start: -0.0130 (m100) cc_final: -0.0433 (p90) REVERT: A 258 TRP cc_start: 0.8326 (t60) cc_final: 0.8058 (t60) REVERT: A 266 MET cc_start: 0.7122 (ppp) cc_final: 0.6835 (mmt) REVERT: C 292 PHE cc_start: 0.7923 (t80) cc_final: 0.7585 (t80) REVERT: D 228 MET cc_start: 0.5347 (mmp) cc_final: 0.4945 (mmp) REVERT: D 266 MET cc_start: 0.7512 (tmm) cc_final: 0.7033 (ttt) REVERT: D 319 VAL cc_start: 0.8641 (t) cc_final: 0.8271 (m) REVERT: E 261 ASN cc_start: 0.8310 (m110) cc_final: 0.7769 (m110) REVERT: E 339 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8536 (mm-40) REVERT: F 292 PHE cc_start: 0.8006 (t80) cc_final: 0.7715 (t80) REVERT: F 482 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8371 (mttt) REVERT: G 266 MET cc_start: 0.6968 (ppp) cc_final: 0.6630 (mmt) REVERT: G 292 PHE cc_start: 0.7999 (t80) cc_final: 0.7557 (t80) outliers start: 32 outliers final: 13 residues processed: 203 average time/residue: 1.1282 time to fit residues: 254.8044 Evaluate side-chains 183 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 416 GLN Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 407 GLN Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 2 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 407 GLN C 339 GLN D 381 ASN D 407 GLN E 396 GLN E 407 GLN F 419 ASN G 407 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14602 Z= 0.247 Angle : 0.621 9.604 19684 Z= 0.305 Chirality : 0.042 0.238 2345 Planarity : 0.003 0.028 2429 Dihedral : 5.890 50.751 2009 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.75 % Allowed : 24.60 % Favored : 72.65 % 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: 0.24 (0.20), residues: 1806 helix: 1.21 (0.17), residues: 1001 sheet: -1.20 (0.29), residues: 315 loop : -0.90 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 258 HIS 0.002 0.001 HIS G 439 PHE 0.040 0.001 PHE D 323 TYR 0.017 0.001 TYR C 256 ARG 0.005 0.000 ARG E 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 1.684 Fit side-chains revert: symmetry clash REVERT: A 258 TRP cc_start: 0.8344 (t60) cc_final: 0.8063 (t60) REVERT: A 266 MET cc_start: 0.7164 (ppp) cc_final: 0.6892 (mmt) REVERT: C 278 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: C 292 PHE cc_start: 0.7932 (t80) cc_final: 0.7585 (t80) REVERT: C 408 ILE cc_start: 0.8674 (tp) cc_final: 0.8422 (tt) REVERT: D 228 MET cc_start: 0.5261 (mmp) cc_final: 0.5030 (mmp) REVERT: D 266 MET cc_start: 0.7384 (tmm) cc_final: 0.6932 (ttt) REVERT: E 339 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8416 (mm-40) REVERT: F 292 PHE cc_start: 0.8008 (t80) cc_final: 0.7698 (t80) REVERT: G 266 MET cc_start: 0.7006 (ppp) cc_final: 0.6720 (mmt) REVERT: G 292 PHE cc_start: 0.8004 (t80) cc_final: 0.7543 (t80) outliers start: 43 outliers final: 14 residues processed: 188 average time/residue: 1.1871 time to fit residues: 246.6399 Evaluate side-chains 181 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 346 MET Chi-restraints excluded: chain G residue 362 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 407 GLN C 339 GLN E 407 GLN G 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14602 Z= 0.286 Angle : 0.656 10.667 19684 Z= 0.318 Chirality : 0.043 0.230 2345 Planarity : 0.003 0.027 2429 Dihedral : 5.989 53.244 2009 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.43 % Allowed : 25.37 % Favored : 72.20 % 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: 0.40 (0.20), residues: 1806 helix: 1.29 (0.17), residues: 1001 sheet: -1.02 (0.29), residues: 308 loop : -0.84 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 258 HIS 0.002 0.001 HIS B 439 PHE 0.035 0.001 PHE D 323 TYR 0.016 0.001 TYR E 256 ARG 0.003 0.000 ARG E 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 1.603 Fit side-chains REVERT: A 258 TRP cc_start: 0.8275 (t60) cc_final: 0.7957 (t60) REVERT: A 266 MET cc_start: 0.7093 (ppp) cc_final: 0.6891 (mmt) REVERT: B 284 ASP cc_start: 0.7652 (p0) cc_final: 0.7390 (p0) REVERT: C 258 TRP cc_start: 0.8223 (OUTLIER) cc_final: 0.7799 (t-100) REVERT: C 278 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: D 228 MET cc_start: 0.5249 (mmp) cc_final: 0.5032 (mmp) REVERT: D 266 MET cc_start: 0.7378 (tmm) cc_final: 0.6933 (ttt) REVERT: E 339 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8393 (mm-40) REVERT: F 266 MET cc_start: 0.7261 (pp-130) cc_final: 0.6866 (mmt) REVERT: F 292 PHE cc_start: 0.7930 (t80) cc_final: 0.7592 (t80) REVERT: F 482 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8403 (mttt) REVERT: G 266 MET cc_start: 0.7151 (ppp) cc_final: 0.6818 (mmt) REVERT: G 292 PHE cc_start: 0.8046 (t80) cc_final: 0.7568 (t80) outliers start: 38 outliers final: 15 residues processed: 193 average time/residue: 1.1974 time to fit residues: 255.3419 Evaluate side-chains 176 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 346 MET Chi-restraints excluded: chain G residue 362 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 80 optimal weight: 0.0970 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 407 GLN E 381 ASN E 396 GLN E 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14602 Z= 0.231 Angle : 0.655 11.281 19684 Z= 0.312 Chirality : 0.042 0.221 2345 Planarity : 0.003 0.027 2429 Dihedral : 5.784 52.646 2009 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.18 % Allowed : 26.14 % Favored : 71.68 % 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: 0.49 (0.20), residues: 1806 helix: 1.34 (0.17), residues: 1001 sheet: -0.94 (0.29), residues: 308 loop : -0.78 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 258 HIS 0.002 0.000 HIS B 439 PHE 0.032 0.001 PHE D 323 TYR 0.016 0.001 TYR C 256 ARG 0.004 0.000 ARG E 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: A 258 TRP cc_start: 0.8276 (t60) cc_final: 0.7957 (t60) REVERT: A 266 MET cc_start: 0.7018 (ppp) cc_final: 0.6811 (mmt) REVERT: C 278 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: D 228 MET cc_start: 0.5250 (mmp) cc_final: 0.5046 (mmp) REVERT: D 266 MET cc_start: 0.7332 (tmm) cc_final: 0.6942 (ttt) REVERT: D 413 MET cc_start: 0.7523 (mmm) cc_final: 0.6988 (mmp) REVERT: E 266 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6165 (mmt) REVERT: E 339 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8367 (mm-40) REVERT: F 266 MET cc_start: 0.7244 (pp-130) cc_final: 0.6752 (mmt) REVERT: F 292 PHE cc_start: 0.7885 (t80) cc_final: 0.7530 (t80) REVERT: F 482 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8381 (mttt) REVERT: G 266 MET cc_start: 0.7025 (ppp) cc_final: 0.6606 (mmt) REVERT: G 292 PHE cc_start: 0.8035 (t80) cc_final: 0.7564 (t80) outliers start: 34 outliers final: 19 residues processed: 189 average time/residue: 1.1318 time to fit residues: 236.8121 Evaluate side-chains 184 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 407 GLN Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 346 MET Chi-restraints excluded: chain G residue 362 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 407 GLN C 387 GLN D 419 ASN E 407 GLN G 419 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14602 Z= 0.205 Angle : 0.641 13.378 19684 Z= 0.307 Chirality : 0.041 0.232 2345 Planarity : 0.003 0.027 2429 Dihedral : 5.622 50.776 2009 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.92 % Allowed : 26.52 % Favored : 71.56 % 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: 0.55 (0.20), residues: 1806 helix: 1.36 (0.17), residues: 1001 sheet: -0.86 (0.29), residues: 308 loop : -0.71 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 258 HIS 0.001 0.000 HIS G 439 PHE 0.028 0.001 PHE D 323 TYR 0.005 0.000 TYR E 256 ARG 0.004 0.000 ARG E 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.909 Fit side-chains REVERT: A 258 TRP cc_start: 0.8276 (t60) cc_final: 0.7957 (t60) REVERT: A 266 MET cc_start: 0.7024 (ppp) cc_final: 0.6775 (mmt) REVERT: A 292 PHE cc_start: 0.7710 (m-80) cc_final: 0.7356 (m-10) REVERT: C 278 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: D 228 MET cc_start: 0.5344 (mmp) cc_final: 0.4949 (mmp) REVERT: D 266 MET cc_start: 0.7284 (tmm) cc_final: 0.6872 (ttt) REVERT: E 266 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6287 (mmt) REVERT: E 339 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8348 (mm-40) REVERT: F 206 TRP cc_start: 0.0618 (m100) cc_final: -0.0091 (p90) REVERT: F 266 MET cc_start: 0.7189 (pp-130) cc_final: 0.6759 (mmt) REVERT: F 292 PHE cc_start: 0.7907 (t80) cc_final: 0.7552 (t80) REVERT: G 266 MET cc_start: 0.6903 (ppp) cc_final: 0.6661 (mmt) REVERT: G 292 PHE cc_start: 0.8033 (t80) cc_final: 0.7553 (t80) outliers start: 30 outliers final: 20 residues processed: 188 average time/residue: 1.1409 time to fit residues: 238.1761 Evaluate side-chains 181 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 346 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN B 407 GLN E 396 GLN E 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14602 Z= 0.310 Angle : 0.694 15.056 19684 Z= 0.329 Chirality : 0.043 0.234 2345 Planarity : 0.003 0.028 2429 Dihedral : 5.868 52.631 2009 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.11 % Allowed : 26.59 % Favored : 71.30 % 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: 0.61 (0.20), residues: 1806 helix: 1.34 (0.17), residues: 1001 sheet: -0.51 (0.32), residues: 273 loop : -0.78 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 258 HIS 0.002 0.001 HIS D 439 PHE 0.028 0.001 PHE D 323 TYR 0.015 0.001 TYR A 256 ARG 0.003 0.000 ARG E 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 1.863 Fit side-chains REVERT: A 258 TRP cc_start: 0.8289 (t60) cc_final: 0.7965 (t60) REVERT: A 266 MET cc_start: 0.7035 (ppp) cc_final: 0.6773 (mmt) REVERT: C 278 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: D 266 MET cc_start: 0.7283 (tmm) cc_final: 0.6875 (ttt) REVERT: E 266 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6417 (mmt) REVERT: E 339 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8330 (mm-40) REVERT: F 206 TRP cc_start: 0.0612 (m100) cc_final: -0.0105 (p90) REVERT: F 266 MET cc_start: 0.7146 (pp-130) cc_final: 0.6785 (mmt) REVERT: F 292 PHE cc_start: 0.7903 (t80) cc_final: 0.7521 (t80) REVERT: G 292 PHE cc_start: 0.8025 (t80) cc_final: 0.7545 (t80) outliers start: 33 outliers final: 23 residues processed: 188 average time/residue: 1.1379 time to fit residues: 237.7204 Evaluate side-chains 186 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 407 GLN Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 346 MET Chi-restraints excluded: chain G residue 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 ASN B 407 GLN E 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14602 Z= 0.182 Angle : 0.645 11.714 19684 Z= 0.308 Chirality : 0.041 0.223 2345 Planarity : 0.003 0.028 2429 Dihedral : 5.560 49.617 2009 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.22 % Allowed : 27.42 % Favored : 71.36 % 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: 1806 helix: 1.42 (0.17), residues: 1001 sheet: -0.29 (0.32), residues: 273 loop : -0.73 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 258 HIS 0.001 0.000 HIS A 439 PHE 0.028 0.001 PHE D 323 TYR 0.010 0.000 TYR A 256 ARG 0.004 0.000 ARG E 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 258 TRP cc_start: 0.8284 (t60) cc_final: 0.7965 (t60) REVERT: A 266 MET cc_start: 0.6983 (ppp) cc_final: 0.6728 (mmt) REVERT: C 278 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: D 228 MET cc_start: 0.5469 (mmp) cc_final: 0.5069 (mmp) REVERT: D 266 MET cc_start: 0.7279 (tmm) cc_final: 0.6871 (ttt) REVERT: E 266 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6440 (mmt) REVERT: E 339 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8282 (mm-40) REVERT: F 206 TRP cc_start: 0.0484 (m100) cc_final: -0.0191 (p90) REVERT: F 266 MET cc_start: 0.7108 (pp-130) cc_final: 0.6766 (mmt) REVERT: F 292 PHE cc_start: 0.7883 (t80) cc_final: 0.7489 (t80) REVERT: G 292 PHE cc_start: 0.8005 (t80) cc_final: 0.7510 (t80) outliers start: 19 outliers final: 10 residues processed: 178 average time/residue: 1.1337 time to fit residues: 223.4863 Evaluate side-chains 173 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 407 GLN Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 346 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN E 396 GLN E 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.112775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.071778 restraints weight = 27453.844| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.87 r_work: 0.2860 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14602 Z= 0.194 Angle : 0.658 12.910 19684 Z= 0.311 Chirality : 0.041 0.222 2345 Planarity : 0.003 0.028 2429 Dihedral : 5.421 47.183 2009 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.28 % Allowed : 27.55 % Favored : 71.17 % 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: 0.83 (0.20), residues: 1806 helix: 1.45 (0.17), residues: 1001 sheet: -0.20 (0.33), residues: 273 loop : -0.64 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 258 HIS 0.001 0.000 HIS G 439 PHE 0.027 0.001 PHE D 323 TYR 0.012 0.001 TYR C 256 ARG 0.004 0.000 ARG E 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4650.53 seconds wall clock time: 83 minutes 32.27 seconds (5012.27 seconds total)