Starting phenix.real_space_refine on Mon Jul 22 09:43:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/07_2024/8sxn_40855_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/07_2024/8sxn_40855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/07_2024/8sxn_40855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/07_2024/8sxn_40855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/07_2024/8sxn_40855_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/07_2024/8sxn_40855_neut.cif" } resolution = 4.04 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= 0.002 sd= 0.028 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 154 5.16 5 C 11278 2.51 5 N 3008 2.21 5 O 3262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17708 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2284 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "B" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2284 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "C" Number of atoms: 6511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6511 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 23, 'TRANS': 792} Chain breaks: 4 Chain: "D" Number of atoms: 6511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6511 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 23, 'TRANS': 792} Chain breaks: 4 Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.47, per 1000 atoms: 0.59 Number of scatterers: 17708 At special positions: 0 Unit cell: (135.616, 172.224, 98.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 6 15.00 O 3262 8.00 N 3008 7.00 C 11278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.99 Conformation dependent library (CDL) restraints added in 3.6 seconds 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 12 sheets defined 49.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.566A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 134 through 154 removed outlier: 3.661A pdb=" N LYS A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 190 through 196 removed outlier: 4.168A pdb=" N SER A 195 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 214 through 232 removed outlier: 3.922A pdb=" N ASP A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 284 through 300 removed outlier: 3.668A pdb=" N CYS A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 79 through 87 removed outlier: 3.510A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 134 through 154 removed outlier: 3.705A pdb=" N LYS B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 190 through 196 removed outlier: 4.190A pdb=" N SER B 195 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 215 through 232 removed outlier: 3.573A pdb=" N ILE B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 284 through 297 Processing helix chain 'C' and resid 136 through 148 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.567A pdb=" N GLU C 356 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLN C 359 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N HIS C 360 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 388 through 402 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 411 through 428 Processing helix chain 'C' and resid 438 through 452 Processing helix chain 'C' and resid 463 through 479 removed outlier: 4.090A pdb=" N GLY C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 492 Processing helix chain 'C' and resid 496 through 505 Processing helix chain 'C' and resid 522 through 534 removed outlier: 3.812A pdb=" N TYR C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 564 Processing helix chain 'C' and resid 567 through 571 Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 592 through 596 Processing helix chain 'C' and resid 597 through 616 Processing helix chain 'C' and resid 627 through 637 Processing helix chain 'C' and resid 639 through 647 Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 659 through 672 Processing helix chain 'C' and resid 731 through 738 Processing helix chain 'C' and resid 754 through 765 Processing helix chain 'C' and resid 785 through 795 removed outlier: 4.196A pdb=" N ASP C 789 " --> pdb=" O GLU C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 824 removed outlier: 3.679A pdb=" N VAL C 820 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 843 through 854 removed outlier: 3.949A pdb=" N SER C 849 " --> pdb=" O GLN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 880 removed outlier: 3.562A pdb=" N LYS C 878 " --> pdb=" O ILE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 909 Processing helix chain 'C' and resid 924 through 937 Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 957 through 966 Processing helix chain 'C' and resid 982 through 994 removed outlier: 3.554A pdb=" N LYS C 994 " --> pdb=" O CYS C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1025 Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 328 through 337 Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.968A pdb=" N GLU D 356 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN D 359 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N HIS D 360 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 388 through 402 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 411 through 428 Processing helix chain 'D' and resid 438 through 452 Processing helix chain 'D' and resid 463 through 479 removed outlier: 4.196A pdb=" N GLY D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 492 Processing helix chain 'D' and resid 496 through 505 Processing helix chain 'D' and resid 522 through 534 removed outlier: 3.942A pdb=" N TYR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 564 Processing helix chain 'D' and resid 567 through 571 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 592 through 596 Processing helix chain 'D' and resid 597 through 617 Processing helix chain 'D' and resid 627 through 637 Processing helix chain 'D' and resid 639 through 647 Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 659 through 672 Processing helix chain 'D' and resid 731 through 738 Processing helix chain 'D' and resid 754 through 765 Processing helix chain 'D' and resid 785 through 795 removed outlier: 4.095A pdb=" N ASP D 789 " --> pdb=" O GLU D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 824 removed outlier: 3.693A pdb=" N VAL D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D 821 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 843 through 854 removed outlier: 3.757A pdb=" N SER D 849 " --> pdb=" O GLN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 880 removed outlier: 3.534A pdb=" N LYS D 878 " --> pdb=" O ILE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 911 removed outlier: 4.477A pdb=" N ALA D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 937 Processing helix chain 'D' and resid 954 through 956 No H-bonds generated for 'chain 'D' and resid 954 through 956' Processing helix chain 'D' and resid 957 through 966 Processing helix chain 'D' and resid 982 through 994 removed outlier: 3.607A pdb=" N LYS D 994 " --> pdb=" O CYS D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1025 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 42 removed outlier: 5.399A pdb=" N ILE A 36 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 52 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG A 42 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 99 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU A 112 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR A 97 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 42 removed outlier: 5.345A pdb=" N ILE B 36 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 52 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG B 42 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU B 112 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR B 97 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AA5, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.675A pdb=" N ILE C 297 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU C 347 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE C 299 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR C 349 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET C 301 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR C 255 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU C 300 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE C 257 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP C 302 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 259 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA7, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AA8, first strand: chain 'C' and resid 652 through 655 removed outlier: 6.614A pdb=" N LEU C 679 " --> pdb=" O ASP C 747 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 889 " --> pdb=" O TYR C 918 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.663A pdb=" N TYR D 255 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU D 300 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE D 257 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP D 302 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE D 259 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AB2, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AB3, first strand: chain 'D' and resid 652 through 655 removed outlier: 6.611A pdb=" N ILE D 653 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU D 679 " --> pdb=" O ASP D 747 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU D 860 " --> pdb=" O GLY D 890 " (cutoff:3.500A) 769 hydrogen bonds defined for protein. 2148 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: 6.60 Time building geometry restraints manager: 7.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2968 1.31 - 1.44: 4591 1.44 - 1.56: 10266 1.56 - 1.69: 23 1.69 - 1.82: 216 Bond restraints: 18064 Sorted by residual: bond pdb=" C08 7YN D1101 " pdb=" C09 7YN D1101 " ideal model delta sigma weight residual 1.340 1.521 -0.181 2.00e-02 2.50e+03 8.19e+01 bond pdb=" C08 7YN C1101 " pdb=" C09 7YN C1101 " ideal model delta sigma weight residual 1.340 1.521 -0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" C14 7YN D1101 " pdb=" N13 7YN D1101 " ideal model delta sigma weight residual 1.349 1.469 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C14 7YN C1101 " pdb=" N13 7YN C1101 " ideal model delta sigma weight residual 1.349 1.463 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C06 7YN C1101 " pdb=" C09 7YN C1101 " ideal model delta sigma weight residual 1.461 1.544 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 18059 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.81: 477 106.81 - 113.91: 10225 113.91 - 121.01: 8783 121.01 - 128.10: 4788 128.10 - 135.20: 117 Bond angle restraints: 24390 Sorted by residual: angle pdb=" PB ATP C1102 " pdb=" O3B ATP C1102 " pdb=" PG ATP C1102 " ideal model delta sigma weight residual 139.87 109.40 30.47 1.00e+00 1.00e+00 9.28e+02 angle pdb=" PB ATP D1102 " pdb=" O3B ATP D1102 " pdb=" PG ATP D1102 " ideal model delta sigma weight residual 139.87 109.46 30.41 1.00e+00 1.00e+00 9.25e+02 angle pdb=" PA ATP D1102 " pdb=" O3A ATP D1102 " pdb=" PB ATP D1102 " ideal model delta sigma weight residual 136.83 111.34 25.49 1.00e+00 1.00e+00 6.50e+02 angle pdb=" PA ATP C1102 " pdb=" O3A ATP C1102 " pdb=" PB ATP C1102 " ideal model delta sigma weight residual 136.83 111.39 25.44 1.00e+00 1.00e+00 6.47e+02 angle pdb=" C5' ATP D1102 " pdb=" O5' ATP D1102 " pdb=" PA ATP D1102 " ideal model delta sigma weight residual 121.27 113.22 8.05 1.00e+00 1.00e+00 6.48e+01 ... (remaining 24385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 10757 27.04 - 54.08: 180 54.08 - 81.12: 61 81.12 - 108.16: 12 108.16 - 135.20: 4 Dihedral angle restraints: 11014 sinusoidal: 4570 harmonic: 6444 Sorted by residual: dihedral pdb=" CA GLN C 624 " pdb=" C GLN C 624 " pdb=" N PRO C 625 " pdb=" CA PRO C 625 " ideal model delta harmonic sigma weight residual 180.00 151.50 28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" C14 7YN C1101 " pdb=" N15 7YN C1101 " pdb=" S17 7YN C1101 " pdb=" O18 7YN C1101 " ideal model delta sinusoidal sigma weight residual 196.22 61.02 135.20 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C14 7YN D1101 " pdb=" N15 7YN D1101 " pdb=" S17 7YN D1101 " pdb=" O18 7YN D1101 " ideal model delta sinusoidal sigma weight residual 196.22 64.01 132.21 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 11011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1554 0.044 - 0.088: 728 0.088 - 0.131: 332 0.131 - 0.175: 105 0.175 - 0.219: 9 Chirality restraints: 2728 Sorted by residual: chirality pdb=" CA PRO A 134 " pdb=" N PRO A 134 " pdb=" C PRO A 134 " pdb=" CB PRO A 134 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C4' ATP C1102 " pdb=" C3' ATP C1102 " pdb=" C5' ATP C1102 " pdb=" O4' ATP C1102 " both_signs ideal model delta sigma weight residual False -2.49 -2.69 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" C4' ATP D1102 " pdb=" C3' ATP D1102 " pdb=" C5' ATP D1102 " pdb=" O4' ATP D1102 " both_signs ideal model delta sigma weight residual False -2.49 -2.69 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 2725 not shown) Planarity restraints: 3076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7YN D1101 " -0.077 2.00e-02 2.50e+03 2.02e-01 1.32e+03 pdb=" C02 7YN D1101 " -0.078 2.00e-02 2.50e+03 pdb=" C03 7YN D1101 " -0.103 2.00e-02 2.50e+03 pdb=" C04 7YN D1101 " -0.078 2.00e-02 2.50e+03 pdb=" C05 7YN D1101 " -0.124 2.00e-02 2.50e+03 pdb=" C06 7YN D1101 " -0.093 2.00e-02 2.50e+03 pdb=" C07 7YN D1101 " -0.059 2.00e-02 2.50e+03 pdb=" C08 7YN D1101 " 0.458 2.00e-02 2.50e+03 pdb=" C09 7YN D1101 " -0.096 2.00e-02 2.50e+03 pdb=" C10 7YN D1101 " -0.060 2.00e-02 2.50e+03 pdb=" C11 7YN D1101 " 0.483 2.00e-02 2.50e+03 pdb=" C12 7YN D1101 " -0.118 2.00e-02 2.50e+03 pdb=" N13 7YN D1101 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN C1101 " 0.075 2.00e-02 2.50e+03 1.97e-01 1.27e+03 pdb=" C02 7YN C1101 " 0.074 2.00e-02 2.50e+03 pdb=" C03 7YN C1101 " 0.108 2.00e-02 2.50e+03 pdb=" C04 7YN C1101 " 0.079 2.00e-02 2.50e+03 pdb=" C05 7YN C1101 " 0.105 2.00e-02 2.50e+03 pdb=" C06 7YN C1101 " 0.103 2.00e-02 2.50e+03 pdb=" C07 7YN C1101 " 0.065 2.00e-02 2.50e+03 pdb=" C08 7YN C1101 " -0.459 2.00e-02 2.50e+03 pdb=" C09 7YN C1101 " 0.096 2.00e-02 2.50e+03 pdb=" C10 7YN C1101 " 0.058 2.00e-02 2.50e+03 pdb=" C11 7YN C1101 " -0.463 2.00e-02 2.50e+03 pdb=" C12 7YN C1101 " 0.105 2.00e-02 2.50e+03 pdb=" N13 7YN C1101 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP C1102 " 0.222 2.00e-02 2.50e+03 8.84e-02 2.15e+02 pdb=" C2 ATP C1102 " -0.031 2.00e-02 2.50e+03 pdb=" C4 ATP C1102 " -0.062 2.00e-02 2.50e+03 pdb=" C5 ATP C1102 " -0.006 2.00e-02 2.50e+03 pdb=" C6 ATP C1102 " 0.036 2.00e-02 2.50e+03 pdb=" C8 ATP C1102 " -0.090 2.00e-02 2.50e+03 pdb=" N1 ATP C1102 " 0.028 2.00e-02 2.50e+03 pdb=" N3 ATP C1102 " -0.074 2.00e-02 2.50e+03 pdb=" N6 ATP C1102 " 0.089 2.00e-02 2.50e+03 pdb=" N7 ATP C1102 " -0.024 2.00e-02 2.50e+03 pdb=" N9 ATP C1102 " -0.089 2.00e-02 2.50e+03 ... (remaining 3073 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 6684 2.87 - 3.38: 17808 3.38 - 3.89: 30520 3.89 - 4.39: 36495 4.39 - 4.90: 57294 Nonbonded interactions: 148801 Sorted by model distance: nonbonded pdb=" OG SER B 187 " pdb=" OG1 THR B 190 " model vdw 2.369 2.440 nonbonded pdb=" OD2 ASP A 78 " pdb=" NZ LYS A 189 " model vdw 2.382 2.520 nonbonded pdb=" O ASP C 949 " pdb=" C ASN C 950 " model vdw 2.399 3.270 nonbonded pdb=" OD2 ASP B 78 " pdb=" NZ LYS B 189 " model vdw 2.400 2.520 nonbonded pdb=" OG SER D 555 " pdb=" N ARG D 556 " model vdw 2.403 2.520 ... (remaining 148796 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 50.840 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.012 0.181 18064 Z= 0.812 Angle : 1.263 30.465 24390 Z= 0.904 Chirality : 0.062 0.219 2728 Planarity : 0.007 0.202 3076 Dihedral : 12.199 135.195 6834 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 1.15 % Allowed : 3.03 % Favored : 95.82 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2176 helix: -0.18 (0.15), residues: 1024 sheet: -0.51 (0.31), residues: 262 loop : -0.00 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP D 611 HIS 0.006 0.001 HIS C 916 PHE 0.020 0.003 PHE C 502 TYR 0.025 0.004 TYR D 443 ARG 0.004 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 409 time to evaluate : 2.090 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: A 34 PHE cc_start: 0.7339 (m-80) cc_final: 0.6926 (m-80) REVERT: A 62 LEU cc_start: 0.7750 (tp) cc_final: 0.3171 (mt) REVERT: A 65 VAL cc_start: 0.8073 (t) cc_final: 0.0643 (t) REVERT: A 109 ILE cc_start: 0.8069 (mt) cc_final: 0.6531 (mt) REVERT: A 140 LYS cc_start: 0.9343 (tttp) cc_final: 0.9104 (ttpt) REVERT: A 142 PHE cc_start: 0.8829 (t80) cc_final: 0.8526 (t80) REVERT: A 158 MET cc_start: 0.6681 (mtm) cc_final: 0.6202 (mtm) REVERT: A 186 PHE cc_start: 0.8800 (m-80) cc_final: 0.8340 (m-80) REVERT: A 226 LEU cc_start: 0.9685 (tp) cc_final: 0.9392 (tp) REVERT: A 236 PHE cc_start: 0.9030 (m-80) cc_final: 0.8773 (m-80) REVERT: A 247 CYS cc_start: 0.8516 (m) cc_final: 0.8229 (t) REVERT: A 286 THR cc_start: 0.9283 (m) cc_final: 0.8879 (t) REVERT: B 34 PHE cc_start: 0.6378 (m-80) cc_final: 0.6048 (m-80) REVERT: B 62 LEU cc_start: 0.7957 (tp) cc_final: 0.3796 (mp) REVERT: B 65 VAL cc_start: 0.8228 (t) cc_final: 0.2226 (t) REVERT: B 104 ASP cc_start: 0.9176 (m-30) cc_final: 0.8963 (t70) REVERT: B 176 LYS cc_start: 0.8552 (mttt) cc_final: 0.8332 (mtpp) REVERT: B 226 LEU cc_start: 0.9642 (tp) cc_final: 0.9356 (tt) REVERT: B 286 THR cc_start: 0.9264 (m) cc_final: 0.8887 (t) REVERT: C 230 ILE cc_start: 0.9210 (mm) cc_final: 0.8900 (mt) REVERT: C 248 LEU cc_start: 0.8082 (tp) cc_final: 0.7391 (mm) REVERT: C 521 ILE cc_start: 0.9156 (pt) cc_final: 0.8635 (mm) REVERT: C 536 LEU cc_start: 0.8468 (mt) cc_final: 0.8192 (pp) REVERT: C 591 TYR cc_start: 0.6877 (m-80) cc_final: 0.6472 (m-10) REVERT: C 637 MET cc_start: 0.8613 (ttm) cc_final: 0.8358 (ttm) REVERT: C 642 PHE cc_start: 0.8475 (t80) cc_final: 0.7625 (t80) REVERT: C 665 VAL cc_start: 0.9590 (t) cc_final: 0.9372 (p) REVERT: C 807 ASP cc_start: 0.8493 (m-30) cc_final: 0.8180 (t70) REVERT: C 846 ASP cc_start: 0.8354 (m-30) cc_final: 0.7831 (t0) REVERT: C 943 LEU cc_start: 0.9266 (tp) cc_final: 0.8958 (tt) REVERT: C 1021 LEU cc_start: 0.9609 (tp) cc_final: 0.9362 (mm) REVERT: C 1025 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8729 (mttp) REVERT: D 230 ILE cc_start: 0.9142 (mm) cc_final: 0.8837 (mt) REVERT: D 240 MET cc_start: 0.8651 (mmm) cc_final: 0.7986 (mmt) REVERT: D 248 LEU cc_start: 0.8089 (tp) cc_final: 0.7723 (mm) REVERT: D 508 PHE cc_start: 0.8130 (m-80) cc_final: 0.7861 (m-10) REVERT: D 521 ILE cc_start: 0.9310 (pt) cc_final: 0.8976 (tp) REVERT: D 591 TYR cc_start: 0.6880 (m-80) cc_final: 0.6650 (m-10) REVERT: D 595 LYS cc_start: 0.8643 (tptt) cc_final: 0.8433 (tptp) REVERT: D 624 GLN cc_start: 0.6675 (mp10) cc_final: 0.6399 (mp10) REVERT: D 807 ASP cc_start: 0.8625 (m-30) cc_final: 0.8235 (t70) REVERT: D 846 ASP cc_start: 0.8290 (m-30) cc_final: 0.7836 (t0) REVERT: D 957 CYS cc_start: 0.8165 (p) cc_final: 0.7551 (p) REVERT: D 961 LEU cc_start: 0.9490 (mt) cc_final: 0.9082 (mt) REVERT: D 1021 LEU cc_start: 0.9592 (tp) cc_final: 0.9361 (mm) outliers start: 1 outliers final: 1 residues processed: 410 average time/residue: 0.3329 time to fit residues: 202.6867 Evaluate side-chains 213 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 1.9990 chunk 165 optimal weight: 0.0170 chunk 91 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 127 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN D 622 GLN ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18064 Z= 0.202 Angle : 0.627 10.357 24390 Z= 0.323 Chirality : 0.041 0.214 2728 Planarity : 0.004 0.030 3076 Dihedral : 9.927 148.089 2474 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.37 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2176 helix: 0.80 (0.16), residues: 1020 sheet: -0.29 (0.33), residues: 244 loop : 0.04 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 478 HIS 0.004 0.001 HIS D 784 PHE 0.029 0.002 PHE C 502 TYR 0.032 0.002 TYR B 141 ARG 0.006 0.000 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 2.096 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: A 109 ILE cc_start: 0.7603 (mt) cc_final: 0.5050 (mt) REVERT: A 112 GLU cc_start: 0.7935 (tt0) cc_final: 0.7699 (tm-30) REVERT: A 140 LYS cc_start: 0.9245 (tttp) cc_final: 0.9031 (ttpt) REVERT: A 142 PHE cc_start: 0.8651 (t80) cc_final: 0.8402 (t80) REVERT: A 152 MET cc_start: 0.9216 (ttm) cc_final: 0.9007 (ttm) REVERT: A 158 MET cc_start: 0.6744 (mtm) cc_final: 0.6444 (mtm) REVERT: A 266 GLU cc_start: 0.7929 (pm20) cc_final: 0.7476 (pm20) REVERT: B 26 MET cc_start: 0.7776 (mmm) cc_final: 0.7353 (mpp) REVERT: B 104 ASP cc_start: 0.9251 (m-30) cc_final: 0.8954 (t0) REVERT: B 110 VAL cc_start: 0.8136 (t) cc_final: 0.6646 (t) REVERT: B 179 ASP cc_start: 0.7968 (p0) cc_final: 0.7566 (m-30) REVERT: B 263 TYR cc_start: 0.8366 (m-80) cc_final: 0.8123 (m-80) REVERT: C 205 MET cc_start: 0.7349 (ttp) cc_final: 0.6886 (tpp) REVERT: C 230 ILE cc_start: 0.9162 (mm) cc_final: 0.8951 (mt) REVERT: C 508 PHE cc_start: 0.8061 (m-80) cc_final: 0.7775 (m-10) REVERT: C 521 ILE cc_start: 0.9225 (pt) cc_final: 0.9011 (tp) REVERT: C 636 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8332 (tp30) REVERT: C 637 MET cc_start: 0.8548 (ttm) cc_final: 0.8283 (ttm) REVERT: C 642 PHE cc_start: 0.8357 (t80) cc_final: 0.7209 (t80) REVERT: C 943 LEU cc_start: 0.9242 (tp) cc_final: 0.8914 (tt) REVERT: C 1025 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8676 (mttp) REVERT: D 140 TYR cc_start: 0.8200 (t80) cc_final: 0.7998 (t80) REVERT: D 230 ILE cc_start: 0.9156 (mm) cc_final: 0.8882 (mt) REVERT: D 240 MET cc_start: 0.8505 (mmm) cc_final: 0.8114 (mmt) REVERT: D 508 PHE cc_start: 0.8221 (m-80) cc_final: 0.7975 (m-10) REVERT: D 521 ILE cc_start: 0.9321 (pt) cc_final: 0.9104 (tp) REVERT: D 595 LYS cc_start: 0.8596 (tptt) cc_final: 0.8347 (tptp) REVERT: D 636 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8250 (tp30) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2856 time to fit residues: 121.4708 Evaluate side-chains 176 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 164 optimal weight: 0.0470 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 214 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS C 360 HIS ** C 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 HIS ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18064 Z= 0.271 Angle : 0.618 10.458 24390 Z= 0.317 Chirality : 0.040 0.141 2728 Planarity : 0.004 0.030 3076 Dihedral : 9.932 148.948 2474 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.64 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 0.42 (0.19), residues: 2176 helix: 0.94 (0.17), residues: 1004 sheet: -0.57 (0.32), residues: 268 loop : -0.03 (0.23), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 478 HIS 0.005 0.001 HIS D 367 PHE 0.039 0.002 PHE D 502 TYR 0.015 0.001 TYR A 49 ARG 0.009 0.000 ARG C 779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.958 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: A 109 ILE cc_start: 0.6747 (mt) cc_final: 0.5424 (mt) REVERT: A 112 GLU cc_start: 0.7967 (tt0) cc_final: 0.7597 (tm-30) REVERT: A 158 MET cc_start: 0.6880 (mtm) cc_final: 0.6616 (mtm) REVERT: A 203 MET cc_start: 0.7223 (mtp) cc_final: 0.6958 (mtp) REVERT: B 65 VAL cc_start: 0.8144 (t) cc_final: 0.5378 (t) REVERT: B 142 PHE cc_start: 0.8686 (t80) cc_final: 0.8382 (t80) REVERT: B 158 MET cc_start: 0.6920 (mpp) cc_final: 0.6567 (mmm) REVERT: B 186 PHE cc_start: 0.8580 (m-80) cc_final: 0.8205 (m-80) REVERT: B 263 TYR cc_start: 0.8532 (m-80) cc_final: 0.8310 (m-80) REVERT: C 230 ILE cc_start: 0.9318 (mm) cc_final: 0.9010 (mt) REVERT: C 521 ILE cc_start: 0.9246 (pt) cc_final: 0.9042 (tp) REVERT: C 600 ILE cc_start: 0.9337 (mm) cc_final: 0.8878 (tp) REVERT: C 943 LEU cc_start: 0.9265 (tp) cc_final: 0.8992 (tt) REVERT: C 978 ASN cc_start: 0.8150 (t0) cc_final: 0.7930 (t0) REVERT: C 1009 TYR cc_start: 0.6520 (t80) cc_final: 0.6314 (t80) REVERT: D 230 ILE cc_start: 0.9238 (mm) cc_final: 0.8969 (mt) REVERT: D 484 PHE cc_start: 0.8742 (m-80) cc_final: 0.8323 (m-10) REVERT: D 502 PHE cc_start: 0.7836 (m-80) cc_final: 0.7441 (m-80) REVERT: D 636 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8292 (tp30) REVERT: D 957 CYS cc_start: 0.8684 (p) cc_final: 0.8182 (p) REVERT: D 1025 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8896 (mmtp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2682 time to fit residues: 90.7324 Evaluate side-chains 165 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18064 Z= 0.189 Angle : 0.556 10.559 24390 Z= 0.282 Chirality : 0.039 0.280 2728 Planarity : 0.004 0.035 3076 Dihedral : 9.903 149.894 2474 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.78 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 0.52 (0.19), residues: 2176 helix: 1.10 (0.17), residues: 988 sheet: -0.62 (0.32), residues: 264 loop : -0.04 (0.23), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 478 HIS 0.003 0.001 HIS C 260 PHE 0.040 0.002 PHE C 502 TYR 0.013 0.001 TYR D 140 ARG 0.004 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.286 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: A 109 ILE cc_start: 0.6377 (mt) cc_final: 0.5555 (mt) REVERT: A 112 GLU cc_start: 0.7834 (tt0) cc_final: 0.7583 (tm-30) REVERT: A 158 MET cc_start: 0.6773 (mtm) cc_final: 0.6518 (mtm) REVERT: A 203 MET cc_start: 0.7214 (mtp) cc_final: 0.6949 (mtp) REVERT: A 263 TYR cc_start: 0.8576 (m-80) cc_final: 0.8250 (m-10) REVERT: B 110 VAL cc_start: 0.8168 (t) cc_final: 0.6896 (t) REVERT: B 142 PHE cc_start: 0.8652 (t80) cc_final: 0.8408 (t80) REVERT: B 158 MET cc_start: 0.6868 (mpp) cc_final: 0.6588 (mmm) REVERT: C 230 ILE cc_start: 0.9276 (mm) cc_final: 0.9027 (mt) REVERT: C 521 ILE cc_start: 0.9232 (pt) cc_final: 0.8940 (mm) REVERT: C 943 LEU cc_start: 0.9225 (tp) cc_final: 0.8952 (tt) REVERT: C 978 ASN cc_start: 0.8130 (t0) cc_final: 0.7913 (t0) REVERT: C 1002 ASN cc_start: 0.7956 (p0) cc_final: 0.7471 (p0) REVERT: D 230 ILE cc_start: 0.9230 (mm) cc_final: 0.8942 (mt) REVERT: D 484 PHE cc_start: 0.8637 (m-80) cc_final: 0.8209 (m-10) REVERT: D 502 PHE cc_start: 0.7676 (m-80) cc_final: 0.7388 (m-80) REVERT: D 636 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8300 (tp30) REVERT: D 957 CYS cc_start: 0.8685 (p) cc_final: 0.7927 (p) REVERT: D 961 LEU cc_start: 0.9364 (mt) cc_final: 0.8919 (mt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2749 time to fit residues: 90.6102 Evaluate side-chains 161 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 5.9990 chunk 119 optimal weight: 0.0050 chunk 3 optimal weight: 20.0000 chunk 156 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN D 995 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18064 Z= 0.255 Angle : 0.595 9.444 24390 Z= 0.300 Chirality : 0.040 0.174 2728 Planarity : 0.004 0.032 3076 Dihedral : 10.003 149.796 2474 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.79 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: 0.33 (0.19), residues: 2176 helix: 0.99 (0.17), residues: 1000 sheet: -0.69 (0.33), residues: 262 loop : -0.23 (0.23), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 478 HIS 0.008 0.001 HIS C 360 PHE 0.022 0.002 PHE C 446 TYR 0.011 0.001 TYR B 287 ARG 0.006 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.966 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: A 109 ILE cc_start: 0.6464 (mt) cc_final: 0.5346 (mt) REVERT: A 112 GLU cc_start: 0.7913 (tt0) cc_final: 0.7621 (tm-30) REVERT: A 152 MET cc_start: 0.9166 (ttm) cc_final: 0.8951 (ttt) REVERT: A 158 MET cc_start: 0.6745 (mtm) cc_final: 0.6399 (mtm) REVERT: A 263 TYR cc_start: 0.8604 (m-80) cc_final: 0.8305 (m-10) REVERT: B 65 VAL cc_start: 0.8082 (t) cc_final: 0.5318 (t) REVERT: B 158 MET cc_start: 0.6882 (mpp) cc_final: 0.6658 (mmm) REVERT: B 186 PHE cc_start: 0.8330 (m-80) cc_final: 0.8025 (m-10) REVERT: B 263 TYR cc_start: 0.8563 (m-80) cc_final: 0.8219 (m-10) REVERT: C 230 ILE cc_start: 0.9349 (mm) cc_final: 0.9052 (mt) REVERT: C 521 ILE cc_start: 0.9235 (pt) cc_final: 0.8911 (mm) REVERT: C 810 LEU cc_start: 0.8780 (mt) cc_final: 0.8429 (mt) REVERT: C 1008 MET cc_start: 0.7884 (mmm) cc_final: 0.7547 (mmm) REVERT: C 1009 TYR cc_start: 0.6384 (t80) cc_final: 0.6068 (t80) REVERT: D 140 TYR cc_start: 0.8424 (t80) cc_final: 0.8222 (t80) REVERT: D 230 ILE cc_start: 0.9297 (mm) cc_final: 0.9016 (mt) REVERT: D 240 MET cc_start: 0.8598 (mmm) cc_final: 0.8350 (tpt) REVERT: D 382 PHE cc_start: 0.8493 (m-10) cc_final: 0.8185 (m-80) REVERT: D 484 PHE cc_start: 0.8760 (m-80) cc_final: 0.8318 (m-10) REVERT: D 502 PHE cc_start: 0.7728 (m-80) cc_final: 0.7461 (m-80) REVERT: D 532 MET cc_start: 0.8996 (tpp) cc_final: 0.8656 (tpp) REVERT: D 810 LEU cc_start: 0.8722 (mt) cc_final: 0.8373 (mt) REVERT: D 957 CYS cc_start: 0.8776 (p) cc_final: 0.8171 (p) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2667 time to fit residues: 85.7631 Evaluate side-chains 157 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 17 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN C 883 GLN D 220 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN D 766 GLN D 883 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 18064 Z= 0.418 Angle : 0.717 9.173 24390 Z= 0.358 Chirality : 0.042 0.155 2728 Planarity : 0.005 0.041 3076 Dihedral : 10.403 149.856 2474 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.57 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 2176 helix: 0.59 (0.16), residues: 1008 sheet: -1.22 (0.31), residues: 276 loop : -0.64 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 478 HIS 0.008 0.001 HIS B 159 PHE 0.034 0.002 PHE C 502 TYR 0.015 0.002 TYR A 287 ARG 0.005 0.001 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8040 (tt0) cc_final: 0.7607 (tm-30) REVERT: A 152 MET cc_start: 0.9148 (ttm) cc_final: 0.8932 (ttt) REVERT: A 263 TYR cc_start: 0.8665 (m-80) cc_final: 0.8381 (m-10) REVERT: B 28 TYR cc_start: 0.5970 (m-10) cc_final: 0.5614 (m-10) REVERT: B 152 MET cc_start: 0.9167 (ttm) cc_final: 0.8916 (ttt) REVERT: B 158 MET cc_start: 0.6998 (mpp) cc_final: 0.6549 (mmm) REVERT: B 203 MET cc_start: 0.7922 (mtp) cc_final: 0.7693 (mtp) REVERT: B 263 TYR cc_start: 0.8642 (m-80) cc_final: 0.8429 (m-80) REVERT: C 230 ILE cc_start: 0.9369 (mm) cc_final: 0.9147 (mt) REVERT: C 239 MET cc_start: 0.9194 (ttp) cc_final: 0.8693 (ttp) REVERT: C 287 ILE cc_start: 0.9479 (mp) cc_final: 0.9237 (pt) REVERT: C 382 PHE cc_start: 0.8669 (m-80) cc_final: 0.8384 (m-80) REVERT: C 484 PHE cc_start: 0.8425 (m-10) cc_final: 0.8175 (m-10) REVERT: C 521 ILE cc_start: 0.9238 (pt) cc_final: 0.8885 (mm) REVERT: C 636 GLU cc_start: 0.8583 (tp30) cc_final: 0.8301 (tp30) REVERT: C 1008 MET cc_start: 0.7957 (mmm) cc_final: 0.7659 (mmm) REVERT: C 1009 TYR cc_start: 0.6447 (t80) cc_final: 0.6231 (t80) REVERT: D 230 ILE cc_start: 0.9357 (mm) cc_final: 0.9096 (mt) REVERT: D 405 LEU cc_start: 0.9465 (tp) cc_final: 0.8854 (tt) REVERT: D 484 PHE cc_start: 0.8913 (m-80) cc_final: 0.8377 (m-10) REVERT: D 636 GLU cc_start: 0.8723 (tp30) cc_final: 0.8408 (tp30) REVERT: D 957 CYS cc_start: 0.8859 (p) cc_final: 0.8327 (p) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2640 time to fit residues: 75.6434 Evaluate side-chains 138 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 210 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 128 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18064 Z= 0.158 Angle : 0.552 8.275 24390 Z= 0.279 Chirality : 0.039 0.147 2728 Planarity : 0.004 0.048 3076 Dihedral : 10.238 151.422 2474 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.61 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 0.09 (0.19), residues: 2176 helix: 0.95 (0.17), residues: 1006 sheet: -1.17 (0.31), residues: 274 loop : -0.43 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 478 HIS 0.004 0.001 HIS A 151 PHE 0.041 0.002 PHE D 502 TYR 0.012 0.001 TYR D 572 ARG 0.005 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.5862 (mt) cc_final: 0.5611 (mt) REVERT: A 112 GLU cc_start: 0.7915 (tt0) cc_final: 0.7608 (tm-30) REVERT: A 152 MET cc_start: 0.9249 (ttm) cc_final: 0.9038 (ttt) REVERT: A 158 MET cc_start: 0.6297 (mtp) cc_final: 0.5922 (mmm) REVERT: A 263 TYR cc_start: 0.8507 (m-80) cc_final: 0.8227 (m-10) REVERT: B 28 TYR cc_start: 0.5984 (m-10) cc_final: 0.5619 (m-10) REVERT: B 152 MET cc_start: 0.9184 (ttm) cc_final: 0.8852 (ttt) REVERT: B 158 MET cc_start: 0.6886 (mpp) cc_final: 0.6573 (mmm) REVERT: B 179 ASP cc_start: 0.6877 (m-30) cc_final: 0.6356 (m-30) REVERT: B 263 TYR cc_start: 0.8539 (m-80) cc_final: 0.8316 (m-80) REVERT: C 205 MET cc_start: 0.7659 (tpp) cc_final: 0.6521 (tpp) REVERT: C 239 MET cc_start: 0.9037 (ttp) cc_final: 0.8620 (ttp) REVERT: C 287 ILE cc_start: 0.9523 (mp) cc_final: 0.9301 (pt) REVERT: C 382 PHE cc_start: 0.8512 (m-80) cc_final: 0.8198 (m-80) REVERT: C 521 ILE cc_start: 0.9207 (pt) cc_final: 0.8899 (mm) REVERT: C 669 CYS cc_start: 0.9444 (m) cc_final: 0.9243 (m) REVERT: C 846 ASP cc_start: 0.8269 (t0) cc_final: 0.7796 (t0) REVERT: D 230 ILE cc_start: 0.9268 (mm) cc_final: 0.9063 (mt) REVERT: D 484 PHE cc_start: 0.8640 (m-80) cc_final: 0.8301 (m-10) REVERT: D 502 PHE cc_start: 0.7633 (m-80) cc_final: 0.7319 (m-80) REVERT: D 505 MET cc_start: 0.7998 (pmm) cc_final: 0.7709 (pmm) REVERT: D 636 GLU cc_start: 0.8645 (tp30) cc_final: 0.8299 (tp30) REVERT: D 1023 GLU cc_start: 0.9294 (mt-10) cc_final: 0.9065 (pp20) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2615 time to fit residues: 78.7633 Evaluate side-chains 145 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 125 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 672 ASN D 845 GLN ** D 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18064 Z= 0.197 Angle : 0.584 9.663 24390 Z= 0.295 Chirality : 0.039 0.181 2728 Planarity : 0.004 0.039 3076 Dihedral : 10.240 151.328 2474 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.84 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 2176 helix: 0.82 (0.17), residues: 1026 sheet: -1.23 (0.32), residues: 272 loop : -0.52 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 243 HIS 0.007 0.001 HIS C 492 PHE 0.039 0.002 PHE D 382 TYR 0.017 0.001 TYR D 140 ARG 0.011 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7955 (tt0) cc_final: 0.7654 (tm-30) REVERT: A 152 MET cc_start: 0.9276 (ttm) cc_final: 0.9066 (ttt) REVERT: A 158 MET cc_start: 0.6364 (mtp) cc_final: 0.5805 (mmm) REVERT: A 219 ILE cc_start: 0.9434 (mm) cc_final: 0.9182 (mm) REVERT: A 263 TYR cc_start: 0.8483 (m-80) cc_final: 0.8175 (m-10) REVERT: B 62 LEU cc_start: 0.5834 (mt) cc_final: 0.4880 (mt) REVERT: B 152 MET cc_start: 0.9226 (ttm) cc_final: 0.8900 (ttt) REVERT: B 158 MET cc_start: 0.6885 (mpp) cc_final: 0.6561 (mmm) REVERT: B 179 ASP cc_start: 0.6898 (m-30) cc_final: 0.5427 (m-30) REVERT: B 263 TYR cc_start: 0.8586 (m-80) cc_final: 0.8375 (m-80) REVERT: C 205 MET cc_start: 0.7405 (tpp) cc_final: 0.7181 (tpp) REVERT: C 208 LEU cc_start: 0.9302 (mt) cc_final: 0.9077 (mt) REVERT: C 239 MET cc_start: 0.8974 (ttp) cc_final: 0.8675 (ttp) REVERT: C 287 ILE cc_start: 0.9526 (mp) cc_final: 0.9305 (pt) REVERT: C 521 ILE cc_start: 0.9202 (pt) cc_final: 0.8912 (mm) REVERT: C 636 GLU cc_start: 0.8695 (tp30) cc_final: 0.8461 (tp30) REVERT: C 987 MET cc_start: 0.8296 (tmm) cc_final: 0.7787 (mmt) REVERT: D 230 ILE cc_start: 0.9293 (mm) cc_final: 0.9068 (mt) REVERT: D 277 MET cc_start: 0.8616 (mpp) cc_final: 0.8352 (mpp) REVERT: D 382 PHE cc_start: 0.8361 (m-80) cc_final: 0.8053 (m-80) REVERT: D 484 PHE cc_start: 0.8687 (m-80) cc_final: 0.8355 (m-10) REVERT: D 502 PHE cc_start: 0.7684 (m-80) cc_final: 0.7389 (m-80) REVERT: D 505 MET cc_start: 0.8041 (pmm) cc_final: 0.7753 (pmm) REVERT: D 636 GLU cc_start: 0.8647 (tp30) cc_final: 0.8326 (tp30) REVERT: D 1023 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9053 (pp20) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2637 time to fit residues: 74.1216 Evaluate side-chains 141 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 183 optimal weight: 0.0980 chunk 195 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18064 Z= 0.188 Angle : 0.577 7.825 24390 Z= 0.293 Chirality : 0.040 0.180 2728 Planarity : 0.004 0.034 3076 Dihedral : 10.249 151.613 2474 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.43 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 2176 helix: 0.84 (0.17), residues: 1026 sheet: -1.21 (0.32), residues: 274 loop : -0.53 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 478 HIS 0.007 0.001 HIS C 492 PHE 0.036 0.002 PHE D 382 TYR 0.015 0.001 TYR A 202 ARG 0.005 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7955 (tt0) cc_final: 0.7708 (tm-30) REVERT: A 152 MET cc_start: 0.9303 (ttm) cc_final: 0.9084 (ttt) REVERT: A 158 MET cc_start: 0.6455 (mtp) cc_final: 0.5812 (mmm) REVERT: A 219 ILE cc_start: 0.9422 (mm) cc_final: 0.9190 (mm) REVERT: A 263 TYR cc_start: 0.8524 (m-80) cc_final: 0.8258 (m-10) REVERT: B 152 MET cc_start: 0.9279 (ttm) cc_final: 0.8904 (ttt) REVERT: B 158 MET cc_start: 0.6835 (mpp) cc_final: 0.6493 (mmm) REVERT: B 263 TYR cc_start: 0.8603 (m-80) cc_final: 0.8376 (m-80) REVERT: C 205 MET cc_start: 0.7780 (tpp) cc_final: 0.7305 (tpp) REVERT: C 208 LEU cc_start: 0.9280 (mt) cc_final: 0.9004 (mt) REVERT: C 239 MET cc_start: 0.8998 (ttp) cc_final: 0.8701 (ttp) REVERT: C 287 ILE cc_start: 0.9527 (mp) cc_final: 0.9323 (pt) REVERT: C 382 PHE cc_start: 0.8597 (m-80) cc_final: 0.8384 (m-80) REVERT: C 484 PHE cc_start: 0.8252 (m-10) cc_final: 0.7916 (m-10) REVERT: C 521 ILE cc_start: 0.9194 (pt) cc_final: 0.8927 (mm) REVERT: C 626 SER cc_start: 0.8260 (p) cc_final: 0.7860 (t) REVERT: C 669 CYS cc_start: 0.9353 (m) cc_final: 0.8970 (m) REVERT: D 230 ILE cc_start: 0.9287 (mm) cc_final: 0.9075 (mt) REVERT: D 484 PHE cc_start: 0.8702 (m-80) cc_final: 0.8375 (m-10) REVERT: D 502 PHE cc_start: 0.7636 (m-80) cc_final: 0.7364 (m-80) REVERT: D 505 MET cc_start: 0.8000 (pmm) cc_final: 0.7758 (pmm) REVERT: D 636 GLU cc_start: 0.8633 (tp30) cc_final: 0.8346 (tp30) REVERT: D 1023 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9046 (pp20) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2470 time to fit residues: 70.8576 Evaluate side-chains 137 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 199 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 17 optimal weight: 30.0000 chunk 133 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18064 Z= 0.153 Angle : 0.553 7.560 24390 Z= 0.279 Chirality : 0.039 0.172 2728 Planarity : 0.003 0.038 3076 Dihedral : 10.184 152.044 2474 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.20 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 0.07 (0.19), residues: 2176 helix: 0.93 (0.17), residues: 1028 sheet: -1.19 (0.32), residues: 274 loop : -0.46 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 243 HIS 0.006 0.001 HIS C 492 PHE 0.030 0.002 PHE D 502 TYR 0.013 0.001 TYR A 202 ARG 0.005 0.000 ARG A 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.5652 (mt) cc_final: 0.5264 (mt) REVERT: A 85 LEU cc_start: 0.9132 (tp) cc_final: 0.8929 (pp) REVERT: A 152 MET cc_start: 0.9332 (ttm) cc_final: 0.9120 (ttt) REVERT: A 158 MET cc_start: 0.6442 (mtp) cc_final: 0.5804 (mmm) REVERT: A 219 ILE cc_start: 0.9375 (mm) cc_final: 0.8925 (mp) REVERT: A 263 TYR cc_start: 0.8540 (m-80) cc_final: 0.8227 (m-10) REVERT: B 152 MET cc_start: 0.9219 (ttm) cc_final: 0.8974 (ttt) REVERT: B 158 MET cc_start: 0.6797 (mpp) cc_final: 0.6448 (mmm) REVERT: B 219 ILE cc_start: 0.9379 (mm) cc_final: 0.9178 (mm) REVERT: B 263 TYR cc_start: 0.8584 (m-80) cc_final: 0.8367 (m-80) REVERT: C 484 PHE cc_start: 0.8276 (m-10) cc_final: 0.7940 (m-10) REVERT: C 521 ILE cc_start: 0.9155 (pt) cc_final: 0.8931 (mm) REVERT: C 626 SER cc_start: 0.8139 (p) cc_final: 0.7763 (t) REVERT: C 978 ASN cc_start: 0.8171 (t0) cc_final: 0.7840 (t0) REVERT: D 230 ILE cc_start: 0.9273 (mm) cc_final: 0.9029 (mt) REVERT: D 484 PHE cc_start: 0.8671 (m-80) cc_final: 0.8336 (m-10) REVERT: D 502 PHE cc_start: 0.7624 (m-80) cc_final: 0.7369 (m-80) REVERT: D 505 MET cc_start: 0.8002 (pmm) cc_final: 0.7767 (pmm) REVERT: D 636 GLU cc_start: 0.8626 (tp30) cc_final: 0.8322 (tp30) REVERT: D 669 CYS cc_start: 0.9300 (m) cc_final: 0.8925 (m) REVERT: D 810 LEU cc_start: 0.8798 (mt) cc_final: 0.8534 (mt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2474 time to fit residues: 76.8390 Evaluate side-chains 148 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 72 optimal weight: 0.0060 chunk 177 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 GLN ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.075352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.057938 restraints weight = 77784.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.059871 restraints weight = 44303.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061187 restraints weight = 30447.212| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18064 Z= 0.189 Angle : 0.563 7.328 24390 Z= 0.284 Chirality : 0.039 0.156 2728 Planarity : 0.004 0.031 3076 Dihedral : 10.214 152.273 2474 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.48 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 2176 helix: 1.01 (0.17), residues: 1014 sheet: -1.22 (0.31), residues: 274 loop : -0.48 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 478 HIS 0.006 0.001 HIS C 492 PHE 0.037 0.002 PHE C 382 TYR 0.013 0.001 TYR A 202 ARG 0.004 0.000 ARG A 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3331.26 seconds wall clock time: 60 minutes 56.37 seconds (3656.37 seconds total)