Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 17:28:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6o_26377/08_2023/7u6o_26377.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6o_26377/08_2023/7u6o_26377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6o_26377/08_2023/7u6o_26377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6o_26377/08_2023/7u6o_26377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6o_26377/08_2023/7u6o_26377.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6o_26377/08_2023/7u6o_26377.pdb" } resolution = 3.2 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= 0.001 sd= 0.037 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 168 5.16 5 C 18618 2.51 5 N 5022 2.21 5 O 5616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 190": "OD1" <-> "OD2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B ASP 463": "OD1" <-> "OD2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C ASP 463": "OD1" <-> "OD2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "E PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 332": "OE1" <-> "OE2" Residue "E PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 190": "OD1" <-> "OD2" Residue "F TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F GLU 459": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 29424 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Chain: "B" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Chain: "C" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Chain: "D" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Chain: "E" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Chain: "F" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Time building chain proxies: 15.36, per 1000 atoms: 0.52 Number of scatterers: 29424 At special positions: 0 Unit cell: (167.932, 178.347, 88.5224, 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 168 16.00 O 5616 8.00 N 5022 7.00 C 18618 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: 12.74 Conformation dependent library (CDL) restraints added in 4.1 seconds 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7032 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 42 sheets defined 54.9% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.857A pdb=" N TYR A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.837A pdb=" N LEU A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 191 through 213 removed outlier: 3.552A pdb=" N MET A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 278 through 293 Processing helix chain 'A' and resid 317 through 338 removed outlier: 3.959A pdb=" N ASP A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 385 through 410 removed outlier: 7.109A pdb=" N ASP A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.633A pdb=" N ASP A 415 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 Processing helix chain 'A' and resid 499 through 523 Processing helix chain 'A' and resid 526 through 539 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 566 through 573 Processing helix chain 'A' and resid 576 through 586 Processing helix chain 'A' and resid 590 through 623 Processing helix chain 'A' and resid 623 through 632 Processing helix chain 'A' and resid 636 through 656 Processing helix chain 'A' and resid 658 through 687 removed outlier: 4.360A pdb=" N MET A 674 " --> pdb=" O ARG A 670 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 703 Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.844A pdb=" N TYR B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.845A pdb=" N LEU B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 191 through 213 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 278 through 293 Processing helix chain 'B' and resid 317 through 338 removed outlier: 3.991A pdb=" N ASP B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 382 Processing helix chain 'B' and resid 385 through 410 removed outlier: 7.141A pdb=" N ASP B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 removed outlier: 3.637A pdb=" N ASP B 415 " --> pdb=" O PRO B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 499 through 523 Processing helix chain 'B' and resid 526 through 539 Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 551 through 560 removed outlier: 3.686A pdb=" N GLU B 555 " --> pdb=" O ALA B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing helix chain 'B' and resid 576 through 586 Processing helix chain 'B' and resid 590 through 623 Processing helix chain 'B' and resid 623 through 632 Processing helix chain 'B' and resid 636 through 656 Processing helix chain 'B' and resid 658 through 672 Processing helix chain 'B' and resid 672 through 687 removed outlier: 3.618A pdb=" N ARG B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 703 Processing helix chain 'C' and resid 44 through 53 removed outlier: 3.853A pdb=" N TYR C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 58 through 65 removed outlier: 3.841A pdb=" N LEU C 62 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 131 through 137 Processing helix chain 'C' and resid 191 through 213 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 278 through 293 removed outlier: 3.503A pdb=" N MET C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 338 removed outlier: 4.042A pdb=" N ASP C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 382 Processing helix chain 'C' and resid 385 through 410 removed outlier: 3.654A pdb=" N LEU C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 417 removed outlier: 3.594A pdb=" N ASP C 415 " --> pdb=" O PRO C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 446 Processing helix chain 'C' and resid 499 through 523 Processing helix chain 'C' and resid 526 through 539 Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 551 through 560 removed outlier: 3.745A pdb=" N GLU C 555 " --> pdb=" O ALA C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 573 Processing helix chain 'C' and resid 576 through 586 Processing helix chain 'C' and resid 590 through 623 Processing helix chain 'C' and resid 623 through 632 Processing helix chain 'C' and resid 636 through 656 Processing helix chain 'C' and resid 658 through 687 removed outlier: 4.177A pdb=" N MET C 674 " --> pdb=" O ARG C 670 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL C 675 " --> pdb=" O LEU C 671 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 687 " --> pdb=" O GLU C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 703 Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.854A pdb=" N TYR D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 56 No H-bonds generated for 'chain 'D' and resid 54 through 56' Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.840A pdb=" N LEU D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN D 64 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 89 Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 191 through 213 removed outlier: 3.556A pdb=" N MET D 213 " --> pdb=" O MET D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 241 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 278 through 293 Processing helix chain 'D' and resid 317 through 338 removed outlier: 3.953A pdb=" N ASP D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 382 Processing helix chain 'D' and resid 385 through 410 removed outlier: 7.107A pdb=" N ASP D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 removed outlier: 3.621A pdb=" N ASP D 415 " --> pdb=" O PRO D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 499 through 523 Processing helix chain 'D' and resid 526 through 539 Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 551 through 560 removed outlier: 3.729A pdb=" N GLU D 555 " --> pdb=" O ALA D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 573 Processing helix chain 'D' and resid 576 through 586 Processing helix chain 'D' and resid 590 through 623 Processing helix chain 'D' and resid 623 through 632 Processing helix chain 'D' and resid 636 through 656 Processing helix chain 'D' and resid 658 through 687 removed outlier: 4.370A pdb=" N MET D 674 " --> pdb=" O ARG D 670 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG D 687 " --> pdb=" O GLU D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 703 Processing helix chain 'E' and resid 44 through 53 removed outlier: 3.852A pdb=" N TYR E 51 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 58 through 65 removed outlier: 3.851A pdb=" N LEU E 62 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN E 64 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 131 through 137 Processing helix chain 'E' and resid 191 through 213 removed outlier: 3.531A pdb=" N MET E 213 " --> pdb=" O MET E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 278 through 293 Processing helix chain 'E' and resid 317 through 338 removed outlier: 4.002A pdb=" N ASP E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 382 Processing helix chain 'E' and resid 385 through 410 removed outlier: 7.103A pdb=" N ASP E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU E 404 " --> pdb=" O LYS E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.631A pdb=" N ASP E 415 " --> pdb=" O PRO E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 499 through 523 Processing helix chain 'E' and resid 526 through 539 Processing helix chain 'E' and resid 540 through 542 No H-bonds generated for 'chain 'E' and resid 540 through 542' Processing helix chain 'E' and resid 551 through 560 removed outlier: 3.695A pdb=" N GLU E 555 " --> pdb=" O ALA E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 573 Processing helix chain 'E' and resid 576 through 586 Processing helix chain 'E' and resid 590 through 623 Processing helix chain 'E' and resid 623 through 632 Processing helix chain 'E' and resid 636 through 656 Processing helix chain 'E' and resid 658 through 672 Processing helix chain 'E' and resid 672 through 687 removed outlier: 3.607A pdb=" N ARG E 687 " --> pdb=" O GLU E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 703 Processing helix chain 'F' and resid 44 through 53 removed outlier: 3.850A pdb=" N TYR F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 58 through 65 removed outlier: 3.841A pdb=" N LEU F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN F 64 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY F 65 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 89 Processing helix chain 'F' and resid 131 through 137 Processing helix chain 'F' and resid 191 through 212 Processing helix chain 'F' and resid 237 through 241 Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 278 through 293 Processing helix chain 'F' and resid 317 through 338 removed outlier: 3.990A pdb=" N ASP F 322 " --> pdb=" O ILE F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 382 Processing helix chain 'F' and resid 385 through 410 removed outlier: 3.570A pdb=" N LEU F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU F 404 " --> pdb=" O LYS F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 417 removed outlier: 3.615A pdb=" N ASP F 415 " --> pdb=" O PRO F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 499 through 523 Processing helix chain 'F' and resid 526 through 539 Processing helix chain 'F' and resid 540 through 542 No H-bonds generated for 'chain 'F' and resid 540 through 542' Processing helix chain 'F' and resid 551 through 560 removed outlier: 3.742A pdb=" N GLU F 555 " --> pdb=" O ALA F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 573 Processing helix chain 'F' and resid 576 through 586 Processing helix chain 'F' and resid 590 through 623 Processing helix chain 'F' and resid 623 through 632 Processing helix chain 'F' and resid 636 through 656 Processing helix chain 'F' and resid 658 through 687 removed outlier: 4.175A pdb=" N MET F 674 " --> pdb=" O ARG F 670 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL F 675 " --> pdb=" O LEU F 671 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 687 " --> pdb=" O GLU F 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 703 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.292A pdb=" N ILE A 168 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 92 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 177 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS A 94 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA A 179 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP A 96 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.292A pdb=" N ILE A 168 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 removed outlier: 3.811A pdb=" N THR A 298 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 316 removed outlier: 3.527A pdb=" N HIS A 358 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 431 Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 458 Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.356A pdb=" N ILE B 168 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 92 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE B 177 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N CYS B 94 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA B 179 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRP B 96 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.356A pdb=" N ILE B 168 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 118 through 120 Processing sheet with id=AB2, first strand: chain 'B' and resid 298 through 301 removed outlier: 3.832A pdb=" N THR B 298 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 315 through 316 removed outlier: 3.525A pdb=" N HIS B 358 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 430 through 431 Processing sheet with id=AB5, first strand: chain 'B' and resid 455 through 458 Processing sheet with id=AB6, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.378A pdb=" N ILE C 168 " --> pdb=" O PHE C 43 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 92 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILE C 177 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS C 94 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA C 179 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TRP C 96 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.378A pdb=" N ILE C 168 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AB9, first strand: chain 'C' and resid 298 through 301 removed outlier: 3.825A pdb=" N THR C 298 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 315 through 316 removed outlier: 3.540A pdb=" N HIS C 358 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 430 through 431 Processing sheet with id=AC3, first strand: chain 'C' and resid 455 through 458 Processing sheet with id=AC4, first strand: chain 'D' and resid 42 through 43 removed outlier: 4.296A pdb=" N ILE D 168 " --> pdb=" O PHE D 43 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 92 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE D 177 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS D 94 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA D 179 " --> pdb=" O CYS D 94 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TRP D 96 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 42 through 43 removed outlier: 4.296A pdb=" N ILE D 168 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 118 through 120 Processing sheet with id=AC7, first strand: chain 'D' and resid 298 through 301 removed outlier: 3.808A pdb=" N THR D 298 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 315 through 316 removed outlier: 3.529A pdb=" N HIS D 358 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 430 through 431 Processing sheet with id=AD1, first strand: chain 'D' and resid 455 through 458 Processing sheet with id=AD2, first strand: chain 'E' and resid 42 through 43 removed outlier: 4.358A pdb=" N ILE E 168 " --> pdb=" O PHE E 43 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL E 92 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE E 177 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS E 94 " --> pdb=" O ILE E 177 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA E 179 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TRP E 96 " --> pdb=" O ALA E 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 42 through 43 removed outlier: 4.358A pdb=" N ILE E 168 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 118 through 120 Processing sheet with id=AD5, first strand: chain 'E' and resid 298 through 301 removed outlier: 3.810A pdb=" N THR E 298 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 315 through 316 removed outlier: 3.522A pdb=" N HIS E 358 " --> pdb=" O GLU E 229 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 430 through 431 Processing sheet with id=AD8, first strand: chain 'E' and resid 455 through 458 Processing sheet with id=AD9, first strand: chain 'F' and resid 42 through 43 removed outlier: 4.256A pdb=" N ILE F 168 " --> pdb=" O PHE F 43 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL F 92 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE F 177 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS F 94 " --> pdb=" O ILE F 177 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA F 179 " --> pdb=" O CYS F 94 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TRP F 96 " --> pdb=" O ALA F 179 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 42 through 43 removed outlier: 4.256A pdb=" N ILE F 168 " --> pdb=" O PHE F 43 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 118 through 120 Processing sheet with id=AE3, first strand: chain 'F' and resid 298 through 301 removed outlier: 3.891A pdb=" N THR F 298 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 315 through 316 removed outlier: 3.546A pdb=" N HIS F 358 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 430 through 431 Processing sheet with id=AE6, first strand: chain 'F' and resid 455 through 458 1726 hydrogen bonds defined for protein. 5016 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: 12.15 Time building geometry restraints manager: 13.68 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: 9722 1.34 - 1.46: 4449 1.46 - 1.58: 15595 1.58 - 1.69: 0 1.69 - 1.81: 294 Bond restraints: 30060 Sorted by residual: bond pdb=" CG1 ILE B 620 " pdb=" CD1 ILE B 620 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.42e+00 bond pdb=" CG1 ILE E 620 " pdb=" CD1 ILE E 620 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.42e+00 bond pdb=" CG1 ILE D 620 " pdb=" CD1 ILE D 620 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.38e+00 bond pdb=" CG1 ILE A 620 " pdb=" CD1 ILE A 620 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.32e+00 bond pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.27e+00 ... (remaining 30055 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.29: 558 104.29 - 111.73: 13779 111.73 - 119.16: 10542 119.16 - 126.60: 15365 126.60 - 134.03: 436 Bond angle restraints: 40680 Sorted by residual: angle pdb=" C VAL C 86 " pdb=" N GLU C 87 " pdb=" CA GLU C 87 " ideal model delta sigma weight residual 122.06 113.75 8.31 1.86e+00 2.89e-01 1.99e+01 angle pdb=" C VAL F 86 " pdb=" N GLU F 87 " pdb=" CA GLU F 87 " ideal model delta sigma weight residual 122.06 114.37 7.69 1.86e+00 2.89e-01 1.71e+01 angle pdb=" N GLU C 87 " pdb=" CA GLU C 87 " pdb=" CB GLU C 87 " ideal model delta sigma weight residual 110.46 115.78 -5.32 1.57e+00 4.06e-01 1.15e+01 angle pdb=" CA MET E 292 " pdb=" CB MET E 292 " pdb=" CG MET E 292 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA MET B 292 " pdb=" CB MET B 292 " pdb=" CG MET B 292 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 ... (remaining 40675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 16154 16.70 - 33.41: 1522 33.41 - 50.11: 317 50.11 - 66.82: 53 66.82 - 83.52: 26 Dihedral angle restraints: 18072 sinusoidal: 7140 harmonic: 10932 Sorted by residual: dihedral pdb=" CA ILE B 226 " pdb=" C ILE B 226 " pdb=" N GLY B 227 " pdb=" CA GLY B 227 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ILE E 226 " pdb=" C ILE E 226 " pdb=" N GLY E 227 " pdb=" CA GLY E 227 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PHE F 589 " pdb=" C PHE F 589 " pdb=" N THR F 590 " pdb=" CA THR F 590 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 18069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3364 0.043 - 0.086: 851 0.086 - 0.130: 214 0.130 - 0.173: 10 0.173 - 0.216: 7 Chirality restraints: 4446 Sorted by residual: chirality pdb=" CA GLU C 87 " pdb=" N GLU C 87 " pdb=" C GLU C 87 " pdb=" CB GLU C 87 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA GLU F 87 " pdb=" N GLU F 87 " pdb=" C GLU F 87 " pdb=" CB GLU F 87 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA GLU D 87 " pdb=" N GLU D 87 " pdb=" C GLU D 87 " pdb=" CB GLU D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 4443 not shown) Planarity restraints: 5346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 83 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C ASP D 83 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP D 83 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP D 84 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 83 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C ASP A 83 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP A 83 " 0.015 2.00e-02 2.50e+03 pdb=" N TRP A 84 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 83 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C ASP E 83 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP E 83 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP E 84 " 0.013 2.00e-02 2.50e+03 ... (remaining 5343 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1080 2.70 - 3.25: 32470 3.25 - 3.80: 53503 3.80 - 4.35: 67127 4.35 - 4.90: 109842 Nonbonded interactions: 264022 Sorted by model distance: nonbonded pdb=" OG1 THR F 365 " pdb=" OD1 ASP F 367 " model vdw 2.152 2.440 nonbonded pdb=" OG1 THR C 365 " pdb=" OD1 ASP C 367 " model vdw 2.152 2.440 nonbonded pdb=" OG1 THR A 365 " pdb=" OD1 ASP A 367 " model vdw 2.153 2.440 nonbonded pdb=" OG1 THR E 365 " pdb=" OD1 ASP E 367 " model vdw 2.155 2.440 nonbonded pdb=" OG1 THR D 365 " pdb=" OD1 ASP D 367 " model vdw 2.156 2.440 ... (remaining 264017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.030 Extract box with map and model: 4.700 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 78.150 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.200 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 30060 Z= 0.207 Angle : 0.576 8.307 40680 Z= 0.308 Chirality : 0.041 0.216 4446 Planarity : 0.004 0.037 5346 Dihedral : 13.726 83.522 11040 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.06 % 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: 0.12 (0.14), residues: 3768 helix: 0.74 (0.12), residues: 1962 sheet: 0.24 (0.28), residues: 402 loop : -0.80 (0.17), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 366 time to evaluate : 3.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.3991 time to fit residues: 237.1071 Evaluate side-chains 304 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 3.203 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 10.0000 chunk 286 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 343 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 GLN ** F 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 30060 Z= 0.326 Angle : 0.621 7.345 40680 Z= 0.323 Chirality : 0.041 0.185 4446 Planarity : 0.004 0.042 5346 Dihedral : 4.074 17.654 4056 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.93 % 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: 0.38 (0.14), residues: 3768 helix: 1.14 (0.11), residues: 1968 sheet: -0.05 (0.31), residues: 288 loop : -0.82 (0.16), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 334 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 345 average time/residue: 0.4001 time to fit residues: 224.4199 Evaluate side-chains 316 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 295 time to evaluate : 3.510 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3078 time to fit residues: 16.0075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 285 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 343 optimal weight: 4.9990 chunk 371 optimal weight: 0.9990 chunk 306 optimal weight: 0.9990 chunk 341 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 30060 Z= 0.171 Angle : 0.561 7.993 40680 Z= 0.288 Chirality : 0.040 0.179 4446 Planarity : 0.004 0.041 5346 Dihedral : 3.968 17.189 4056 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 1.06 % 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 (0.14), residues: 3768 helix: 1.34 (0.11), residues: 1974 sheet: 0.74 (0.31), residues: 282 loop : -0.94 (0.16), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 348 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 10 residues processed: 370 average time/residue: 0.3963 time to fit residues: 241.7771 Evaluate side-chains 319 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 309 time to evaluate : 3.234 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3108 time to fit residues: 9.8139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 178 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 345 optimal weight: 8.9990 chunk 365 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 327 optimal weight: 0.8980 chunk 98 optimal weight: 30.0000 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 30060 Z= 0.236 Angle : 0.575 8.935 40680 Z= 0.296 Chirality : 0.040 0.181 4446 Planarity : 0.004 0.039 5346 Dihedral : 3.940 20.547 4056 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.93 % 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: 0.62 (0.14), residues: 3768 helix: 1.39 (0.11), residues: 1974 sheet: 0.06 (0.29), residues: 318 loop : -0.82 (0.16), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 326 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 343 average time/residue: 0.4487 time to fit residues: 250.1621 Evaluate side-chains 320 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 302 time to evaluate : 3.730 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2988 time to fit residues: 14.5050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 311 optimal weight: 8.9990 chunk 252 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 327 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 30060 Z= 0.305 Angle : 0.609 8.209 40680 Z= 0.312 Chirality : 0.041 0.194 4446 Planarity : 0.004 0.044 5346 Dihedral : 3.979 19.929 4056 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.61 % 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: 0.63 (0.14), residues: 3768 helix: 1.41 (0.12), residues: 1974 sheet: -0.02 (0.29), residues: 318 loop : -0.80 (0.16), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 319 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 334 average time/residue: 0.4357 time to fit residues: 236.2153 Evaluate side-chains 307 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 300 time to evaluate : 3.933 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3208 time to fit residues: 9.2469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 2.9990 chunk 329 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 365 optimal weight: 10.0000 chunk 303 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 30060 Z= 0.191 Angle : 0.592 9.004 40680 Z= 0.300 Chirality : 0.040 0.197 4446 Planarity : 0.004 0.043 5346 Dihedral : 3.948 19.244 4056 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.83 % 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: 0.63 (0.14), residues: 3768 helix: 1.40 (0.11), residues: 1980 sheet: 0.67 (0.31), residues: 282 loop : -0.95 (0.16), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 337 time to evaluate : 3.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 354 average time/residue: 0.4012 time to fit residues: 233.5097 Evaluate side-chains 329 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 318 time to evaluate : 3.754 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2846 time to fit residues: 10.6238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 307 optimal weight: 0.2980 chunk 204 optimal weight: 8.9990 chunk 364 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 30060 Z= 0.211 Angle : 0.614 12.562 40680 Z= 0.311 Chirality : 0.040 0.205 4446 Planarity : 0.004 0.041 5346 Dihedral : 3.958 19.092 4056 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.64 % 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: 0.62 (0.14), residues: 3768 helix: 1.38 (0.11), residues: 1980 sheet: 0.69 (0.31), residues: 282 loop : -0.94 (0.16), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 330 time to evaluate : 3.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 346 average time/residue: 0.4089 time to fit residues: 231.9398 Evaluate side-chains 315 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 309 time to evaluate : 3.247 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2892 time to fit residues: 7.4248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.5980 chunk 145 optimal weight: 7.9990 chunk 217 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 231 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30060 Z= 0.198 Angle : 0.625 13.245 40680 Z= 0.313 Chirality : 0.040 0.208 4446 Planarity : 0.004 0.039 5346 Dihedral : 3.949 19.181 4056 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.51 % 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: 0.62 (0.14), residues: 3768 helix: 1.37 (0.11), residues: 1980 sheet: 0.71 (0.31), residues: 282 loop : -0.93 (0.16), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 333 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 343 average time/residue: 0.4122 time to fit residues: 230.1101 Evaluate side-chains 322 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 313 time to evaluate : 3.652 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2846 time to fit residues: 9.6172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 9.9990 chunk 349 optimal weight: 6.9990 chunk 318 optimal weight: 7.9990 chunk 339 optimal weight: 8.9990 chunk 348 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 30060 Z= 0.373 Angle : 0.709 12.631 40680 Z= 0.358 Chirality : 0.042 0.215 4446 Planarity : 0.004 0.039 5346 Dihedral : 4.135 19.278 4056 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3768 helix: 1.27 (0.12), residues: 1980 sheet: -0.06 (0.27), residues: 390 loop : -0.81 (0.17), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 313 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 321 average time/residue: 0.3936 time to fit residues: 206.2037 Evaluate side-chains 306 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 298 time to evaluate : 3.750 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2865 time to fit residues: 9.1709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 10.0000 chunk 222 optimal weight: 0.8980 chunk 359 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 376 optimal weight: 0.8980 chunk 346 optimal weight: 7.9990 chunk 299 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 30060 Z= 0.188 Angle : 0.673 13.164 40680 Z= 0.336 Chirality : 0.041 0.221 4446 Planarity : 0.004 0.047 5346 Dihedral : 4.074 21.316 4056 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.16 % 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 (0.14), residues: 3768 helix: 1.34 (0.11), residues: 1986 sheet: 0.48 (0.31), residues: 282 loop : -0.96 (0.16), residues: 1500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 324 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 325 average time/residue: 0.4144 time to fit residues: 219.5078 Evaluate side-chains 314 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 309 time to evaluate : 3.503 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2792 time to fit residues: 7.3416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 1.9990 chunk 238 optimal weight: 20.0000 chunk 319 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.095798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.076092 restraints weight = 98936.237| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 4.08 r_work: 0.3421 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 30060 Z= 0.233 Angle : 0.678 14.290 40680 Z= 0.338 Chirality : 0.041 0.217 4446 Planarity : 0.004 0.042 5346 Dihedral : 4.052 21.511 4056 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.06 % 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 (0.14), residues: 3768 helix: 1.35 (0.11), residues: 1992 sheet: 0.47 (0.31), residues: 282 loop : -0.94 (0.16), residues: 1494 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5625.82 seconds wall clock time: 104 minutes 33.38 seconds (6273.38 seconds total)