Starting phenix.real_space_refine (version: dev) on Tue Dec 13 07:24:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/12_2022/6vxn_21445_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/12_2022/6vxn_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_21445/12_2022/6vxn_21445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/12_2022/6vxn_21445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/12_2022/6vxn_21445_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/12_2022/6vxn_21445_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Convert atoms to be neutral 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 7.93, per 1000 atoms: 0.55 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: 6.02 Conformation dependent library (CDL) restraints added in 2.2 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: 1.16 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: 4.40 Time building geometry restraints manager: 6.42 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 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. 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: 1.690 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: 6.170 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.130 Process input model: 38.820 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 % 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 *********************** 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 : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 5 residues processed: 310 average time/residue: 1.2788 time to fit residues: 432.0843 Evaluate side-chains 190 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 185 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 5 average time/residue: 0.2407 time to fit residues: 4.1482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 261 ASN C 381 ASN C 416 GLN C 457 ASN D 457 ASN E 457 ASN F 457 ASN G 457 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2492 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= 0.223 Angle : 0.644 8.759 19684 Z= 0.323 Chirality : 0.043 0.228 2345 Planarity : 0.005 0.032 2429 Dihedral : 7.038 53.566 2009 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 1806 helix: -0.18 (0.16), residues: 1015 sheet: -1.61 (0.25), residues: 350 loop : -1.84 (0.24), residues: 441 *********************** 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 232 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 11 residues processed: 212 average time/residue: 1.0630 time to fit residues: 251.5616 Evaluate side-chains 195 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 7 average time/residue: 0.8689 time to fit residues: 9.3256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 137 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 45 optimal weight: 0.5980 chunk 165 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 164 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN C 358 GLN C 407 GLN C 419 ASN E 224 GLN F 381 ASN G 358 GLN G 470 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2909 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= 0.169 Angle : 0.596 8.855 19684 Z= 0.294 Chirality : 0.042 0.214 2345 Planarity : 0.004 0.034 2429 Dihedral : 6.178 51.917 2009 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.54 % 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: -0.39 (0.19), residues: 1806 helix: 0.79 (0.17), residues: 994 sheet: -1.54 (0.26), residues: 350 loop : -1.27 (0.25), residues: 462 *********************** 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 220 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 208 average time/residue: 1.1227 time to fit residues: 259.2918 Evaluate side-chains 177 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 1.992 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 1.1674 time to fit residues: 4.9387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 8.9990 chunk 124 optimal weight: 0.0570 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 0.0470 chunk 79 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN A 416 GLN B 407 GLN C 407 GLN E 419 ASN G 358 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 14602 Z= 0.228 Angle : 0.617 9.423 19684 Z= 0.305 Chirality : 0.042 0.233 2345 Planarity : 0.004 0.027 2429 Dihedral : 5.961 51.072 2009 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 2.37 % 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: 0.03 (0.20), residues: 1806 helix: 1.06 (0.17), residues: 1001 sheet: -1.26 (0.29), residues: 315 loop : -1.05 (0.26), residues: 490 *********************** 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 225 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 1.956 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 10 residues processed: 205 average time/residue: 1.0977 time to fit residues: 250.8981 Evaluate side-chains 179 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 1.986 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 1.1330 time to fit residues: 4.9396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 0.4980 chunk 157 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN A 416 GLN A 419 ASN B 407 GLN B 419 ASN C 407 GLN D 381 ASN D 419 ASN E 261 ASN F 419 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 14602 Z= 0.186 Angle : 0.609 9.547 19684 Z= 0.298 Chirality : 0.042 0.238 2345 Planarity : 0.003 0.026 2429 Dihedral : 5.662 48.860 2009 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 1.60 % 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: 0.31 (0.20), residues: 1806 helix: 1.25 (0.17), residues: 1001 sheet: -1.16 (0.29), residues: 315 loop : -0.86 (0.26), residues: 490 *********************** 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 199 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 189 average time/residue: 1.1011 time to fit residues: 231.7529 Evaluate side-chains 178 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.6719 time to fit residues: 6.2866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 176 optimal weight: 0.0010 chunk 146 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN D 407 GLN E 224 GLN E 396 GLN E 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 14602 Z= 0.188 Angle : 0.612 9.994 19684 Z= 0.298 Chirality : 0.041 0.224 2345 Planarity : 0.003 0.024 2429 Dihedral : 5.479 45.906 2009 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 1.35 % 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: 1.33 (0.17), residues: 1001 sheet: -0.91 (0.29), residues: 308 loop : -0.77 (0.27), residues: 497 *********************** 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 192 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 184 average time/residue: 1.1671 time to fit residues: 238.4998 Evaluate side-chains 170 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.6529 time to fit residues: 4.7250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 0.0670 overall best weight: 0.5520 ------------------------------------------------------------------------------- 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 D 396 GLN D 407 GLN E 381 ASN E 470 GLN E 484 HIS F 416 GLN G 419 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 14602 Z= 0.161 Angle : 0.613 10.962 19684 Z= 0.296 Chirality : 0.041 0.217 2345 Planarity : 0.003 0.025 2429 Dihedral : 5.161 38.679 2009 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1806 helix: 1.41 (0.17), residues: 1001 sheet: -1.03 (0.28), residues: 343 loop : -0.55 (0.27), residues: 462 *********************** 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 189 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 184 average time/residue: 1.0870 time to fit residues: 222.7010 Evaluate side-chains 173 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 2 average time/residue: 0.7146 time to fit residues: 3.8245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 0.0980 chunk 16 optimal weight: 0.3980 chunk 137 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 407 GLN B 407 GLN E 396 GLN E 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4181 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= 0.263 Angle : 0.638 10.601 19684 Z= 0.311 Chirality : 0.042 0.221 2345 Planarity : 0.003 0.026 2429 Dihedral : 5.472 40.549 2009 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1806 helix: 1.39 (0.17), residues: 1001 sheet: -0.78 (0.30), residues: 308 loop : -0.58 (0.28), residues: 497 *********************** 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 187 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.940 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 181 average time/residue: 1.0696 time to fit residues: 217.1403 Evaluate side-chains 171 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1755 time to fit residues: 2.6863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4280 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= 0.213 Angle : 0.651 12.055 19684 Z= 0.312 Chirality : 0.042 0.220 2345 Planarity : 0.003 0.027 2429 Dihedral : 5.365 39.110 2009 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1806 helix: 1.42 (0.17), residues: 1001 sheet: -0.69 (0.30), residues: 308 loop : -0.52 (0.28), residues: 497 *********************** 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 181 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.740 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 177 average time/residue: 1.0532 time to fit residues: 208.0238 Evaluate side-chains 171 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 1.903 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 2.4938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 396 GLN G 358 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 14602 Z= 0.290 Angle : 0.670 10.985 19684 Z= 0.324 Chirality : 0.043 0.225 2345 Planarity : 0.003 0.028 2429 Dihedral : 5.644 41.669 2009 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.96 % 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: 0.79 (0.20), residues: 1806 helix: 1.43 (0.17), residues: 1001 sheet: -0.30 (0.32), residues: 273 loop : -0.66 (0.27), residues: 532 ********************** 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 176 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.964 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 173 average time/residue: 1.0954 time to fit residues: 211.3748 Evaluate side-chains 171 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.761 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 1 average time/residue: 0.2592 time to fit residues: 2.7560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 144 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 148 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 381 ASN B 407 GLN G 484 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.115058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.073238 restraints weight = 27407.475| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.87 r_work: 0.2871 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14602 Z= 0.167 Angle : 0.650 12.087 19684 Z= 0.310 Chirality : 0.041 0.216 2345 Planarity : 0.003 0.026 2429 Dihedral : 5.163 34.510 2009 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.96 % 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: 0.92 (0.20), residues: 1806 helix: 1.50 (0.17), residues: 1001 sheet: -0.15 (0.33), residues: 273 loop : -0.57 (0.27), residues: 532 =============================================================================== Job complete usr+sys time: 4499.25 seconds wall clock time: 81 minutes 28.47 seconds (4888.47 seconds total)