Starting phenix.real_space_refine on Fri Feb 23 22:52:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yep_33774/02_2024/7yep_33774_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yep_33774/02_2024/7yep_33774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yep_33774/02_2024/7yep_33774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yep_33774/02_2024/7yep_33774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yep_33774/02_2024/7yep_33774_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yep_33774/02_2024/7yep_33774_trim_updated.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians S 108 5.16 5 B 4 2.79 5 C 13120 2.51 5 N 3376 2.21 5 O 3440 1.98 5 H 20284 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A GLU 667": "OE1" <-> "OE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 642": "OE1" <-> "OE2" Residue "B ASP 650": "OD1" <-> "OD2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 609": "OE1" <-> "OE2" Residue "C TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 650": "OD1" <-> "OD2" Residue "C GLU 667": "OE1" <-> "OE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 464": "OD1" <-> "OD2" Residue "D PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 642": "OE1" <-> "OE2" Residue "D ASP 650": "OD1" <-> "OD2" Residue "D GLU 667": "OE1" <-> "OE2" Residue "D PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40332 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.33, per 1000 atoms: 0.43 Number of scatterers: 40332 At special positions: 0 Unit cell: (147.87, 147.87, 118.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 O 3440 8.00 N 3376 7.00 C 13120 6.00 B 4 5.00 H 20284 1.00 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: 31.24 Conformation dependent library (CDL) restraints added in 4.2 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 4 sheets defined 55.3% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 129 through 140 Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.876A pdb=" N LYS A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 218 through 226 removed outlier: 3.763A pdb=" N THR A 222 " --> pdb=" O TRP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 256 through 276 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 371 through 407 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 424 through 452 Processing helix chain 'A' and resid 468 through 486 Processing helix chain 'A' and resid 492 through 512 removed outlier: 4.429A pdb=" N LEU A 508 " --> pdb=" O TRP A 504 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.560A pdb=" N ILE A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 520 " --> pdb=" O HIS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 632 through 646 Processing helix chain 'A' and resid 649 through 667 Processing helix chain 'A' and resid 710 through 712 No H-bonds generated for 'chain 'A' and resid 710 through 712' Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 129 through 140 Proline residue: B 133 - end of helix Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 162 through 169 removed outlier: 3.853A pdb=" N LYS B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 218 through 226 removed outlier: 3.727A pdb=" N THR B 222 " --> pdb=" O TRP B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 256 through 276 Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 371 through 407 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 424 through 452 Processing helix chain 'B' and resid 462 through 465 No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'B' and resid 468 through 486 Processing helix chain 'B' and resid 492 through 512 removed outlier: 4.444A pdb=" N LEU B 508 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 531 removed outlier: 3.558A pdb=" N ILE B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR B 520 " --> pdb=" O HIS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 552 Processing helix chain 'B' and resid 588 through 600 Processing helix chain 'B' and resid 614 through 628 Processing helix chain 'B' and resid 632 through 646 Processing helix chain 'B' and resid 649 through 667 Processing helix chain 'B' and resid 710 through 712 No H-bonds generated for 'chain 'B' and resid 710 through 712' Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 90 through 96 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 115 through 121 Processing helix chain 'C' and resid 129 through 140 Proline residue: C 133 - end of helix Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.871A pdb=" N LYS C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 218 through 226 removed outlier: 3.762A pdb=" N THR C 222 " --> pdb=" O TRP C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 256 through 276 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 304 through 310 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 371 through 407 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 424 through 452 Processing helix chain 'C' and resid 468 through 486 Processing helix chain 'C' and resid 492 through 512 removed outlier: 4.424A pdb=" N LEU C 508 " --> pdb=" O TRP C 504 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 531 removed outlier: 3.584A pdb=" N ILE C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR C 520 " --> pdb=" O HIS C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 Processing helix chain 'C' and resid 588 through 600 Processing helix chain 'C' and resid 614 through 628 Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 649 through 667 Processing helix chain 'C' and resid 710 through 712 No H-bonds generated for 'chain 'C' and resid 710 through 712' Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 90 through 97 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 115 through 121 Processing helix chain 'D' and resid 129 through 140 Proline residue: D 133 - end of helix Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 162 through 169 removed outlier: 3.856A pdb=" N LYS D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 218 through 226 removed outlier: 3.703A pdb=" N THR D 222 " --> pdb=" O TRP D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 Processing helix chain 'D' and resid 256 through 276 Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 304 through 310 Processing helix chain 'D' and resid 351 through 357 Processing helix chain 'D' and resid 364 through 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 371 through 407 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 424 through 452 Processing helix chain 'D' and resid 468 through 486 Processing helix chain 'D' and resid 492 through 512 removed outlier: 4.447A pdb=" N LEU D 508 " --> pdb=" O TRP D 504 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR D 509 " --> pdb=" O LEU D 505 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR D 510 " --> pdb=" O ASN D 506 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 531 removed outlier: 3.566A pdb=" N ILE D 519 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR D 520 " --> pdb=" O HIS D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 Processing helix chain 'D' and resid 588 through 600 Processing helix chain 'D' and resid 614 through 628 Processing helix chain 'D' and resid 632 through 646 Processing helix chain 'D' and resid 649 through 667 Processing helix chain 'D' and resid 710 through 712 No H-bonds generated for 'chain 'D' and resid 710 through 712' Processing sheet with id= A, first strand: chain 'A' and resid 333 through 339 Processing sheet with id= B, first strand: chain 'B' and resid 333 through 339 Processing sheet with id= C, first strand: chain 'C' and resid 333 through 339 Processing sheet with id= D, first strand: chain 'D' and resid 333 through 339 901 hydrogen bonds defined for protein. 2625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.75 Time building geometry restraints manager: 32.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 20228 1.03 - 1.22: 56 1.22 - 1.42: 8776 1.42 - 1.61: 11620 1.61 - 1.81: 160 Bond restraints: 40840 Sorted by residual: bond pdb=" C02 FZ4 B1001 " pdb=" C03 FZ4 B1001 " ideal model delta sigma weight residual 1.400 1.367 0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C02 FZ4 D1001 " pdb=" C03 FZ4 D1001 " ideal model delta sigma weight residual 1.400 1.368 0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C02 FZ4 A1001 " pdb=" C03 FZ4 A1001 " ideal model delta sigma weight residual 1.400 1.368 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" C02 FZ4 C1001 " pdb=" C03 FZ4 C1001 " ideal model delta sigma weight residual 1.400 1.368 0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" N VAL A 335 " pdb=" CA VAL A 335 " ideal model delta sigma weight residual 1.474 1.452 0.022 1.57e-02 4.06e+03 1.98e+00 ... (remaining 40835 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.28: 291 105.28 - 112.47: 46758 112.47 - 119.66: 10778 119.66 - 126.85: 15579 126.85 - 134.04: 350 Bond angle restraints: 73756 Sorted by residual: angle pdb=" N VAL C 335 " pdb=" CA VAL C 335 " pdb=" C VAL C 335 " ideal model delta sigma weight residual 106.21 109.65 -3.44 1.07e+00 8.73e-01 1.03e+01 angle pdb=" C08 FZ4 D1001 " pdb=" B01 FZ4 D1001 " pdb=" O14 FZ4 D1001 " ideal model delta sigma weight residual 123.29 114.94 8.35 3.00e+00 1.11e-01 7.75e+00 angle pdb=" C08 FZ4 A1001 " pdb=" B01 FZ4 A1001 " pdb=" O14 FZ4 A1001 " ideal model delta sigma weight residual 123.29 115.51 7.78 3.00e+00 1.11e-01 6.72e+00 angle pdb=" C SER C 465 " pdb=" N TYR C 466 " pdb=" CA TYR C 466 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.23e+00 angle pdb=" CB MET D 523 " pdb=" CG MET D 523 " pdb=" SD MET D 523 " ideal model delta sigma weight residual 112.70 105.30 7.40 3.00e+00 1.11e-01 6.09e+00 ... (remaining 73751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 17834 22.53 - 45.07: 940 45.07 - 67.60: 247 67.60 - 90.13: 16 90.13 - 112.66: 3 Dihedral angle restraints: 19040 sinusoidal: 10212 harmonic: 8828 Sorted by residual: dihedral pdb=" CA ARG B 512 " pdb=" C ARG B 512 " pdb=" N GLY B 513 " pdb=" CA GLY B 513 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU B 508 " pdb=" C LEU B 508 " pdb=" N TYR B 509 " pdb=" CA TYR B 509 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ARG A 512 " pdb=" C ARG A 512 " pdb=" N GLY A 513 " pdb=" CA GLY A 513 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 19037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1945 0.029 - 0.058: 818 0.058 - 0.087: 265 0.087 - 0.116: 99 0.116 - 0.145: 13 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA VAL D 335 " pdb=" N VAL D 335 " pdb=" C VAL D 335 " pdb=" CB VAL D 335 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL B 335 " pdb=" N VAL B 335 " pdb=" C VAL B 335 " pdb=" CB VAL B 335 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CB VAL B 483 " pdb=" CA VAL B 483 " pdb=" CG1 VAL B 483 " pdb=" CG2 VAL B 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 3137 not shown) Planarity restraints: 5808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 C1001 " 0.572 2.00e-02 2.50e+03 3.74e-01 2.45e+03 pdb=" C02 FZ4 C1001 " -0.315 2.00e-02 2.50e+03 pdb=" C03 FZ4 C1001 " -0.547 2.00e-02 2.50e+03 pdb=" C04 FZ4 C1001 " 0.128 2.00e-02 2.50e+03 pdb=" C05 FZ4 C1001 " 0.424 2.00e-02 2.50e+03 pdb=" C06 FZ4 C1001 " -0.018 2.00e-02 2.50e+03 pdb=" C07 FZ4 C1001 " -0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 D1001 " 0.554 2.00e-02 2.50e+03 3.66e-01 2.35e+03 pdb=" C02 FZ4 D1001 " -0.309 2.00e-02 2.50e+03 pdb=" C03 FZ4 D1001 " -0.549 2.00e-02 2.50e+03 pdb=" C04 FZ4 D1001 " 0.144 2.00e-02 2.50e+03 pdb=" C05 FZ4 D1001 " 0.405 2.00e-02 2.50e+03 pdb=" C06 FZ4 D1001 " -0.024 2.00e-02 2.50e+03 pdb=" C07 FZ4 D1001 " -0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 B1001 " -0.550 2.00e-02 2.50e+03 3.59e-01 2.25e+03 pdb=" C02 FZ4 B1001 " 0.319 2.00e-02 2.50e+03 pdb=" C03 FZ4 B1001 " 0.534 2.00e-02 2.50e+03 pdb=" C04 FZ4 B1001 " -0.150 2.00e-02 2.50e+03 pdb=" C05 FZ4 B1001 " -0.380 2.00e-02 2.50e+03 pdb=" C06 FZ4 B1001 " 0.016 2.00e-02 2.50e+03 pdb=" C07 FZ4 B1001 " 0.211 2.00e-02 2.50e+03 ... (remaining 5805 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 702 2.06 - 2.70: 66556 2.70 - 3.33: 122214 3.33 - 3.97: 152016 3.97 - 4.60: 242455 Nonbonded interactions: 583943 Sorted by model distance: nonbonded pdb=" O TRP C 452 " pdb="HH11 ARG C 455 " model vdw 1.426 1.850 nonbonded pdb=" O ILE C 167 " pdb="HE22 GLN C 217 " model vdw 1.523 1.850 nonbonded pdb=" O ILE A 167 " pdb="HE22 GLN A 217 " model vdw 1.532 1.850 nonbonded pdb=" OD1 ASN B 227 " pdb=" H GLN B 230 " model vdw 1.585 1.850 nonbonded pdb=" OD1 ASN D 227 " pdb=" H GLN D 230 " model vdw 1.590 1.850 ... (remaining 583938 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.610 Extract box with map and model: 5.410 Check model and map are aligned: 0.570 Set scattering table: 0.330 Process input model: 119.270 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 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 : 0.006 0.070 20556 Z= 0.364 Angle : 0.669 8.352 27884 Z= 0.370 Chirality : 0.038 0.145 3140 Planarity : 0.015 0.374 3440 Dihedral : 14.193 112.664 7424 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.21 (0.17), residues: 2432 helix: 1.39 (0.14), residues: 1428 sheet: -1.89 (0.51), residues: 68 loop : -1.75 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 449 HIS 0.005 0.001 HIS C 516 PHE 0.015 0.002 PHE A 402 TYR 0.022 0.002 TYR C 492 ARG 0.009 0.001 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 3.072 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 305 ILE cc_start: 0.8635 (tp) cc_final: 0.8416 (tp) REVERT: C 272 MET cc_start: 0.4960 (mtt) cc_final: 0.4674 (ttm) REVERT: C 305 ILE cc_start: 0.8634 (tp) cc_final: 0.8389 (tp) REVERT: D 305 ILE cc_start: 0.8580 (tp) cc_final: 0.8375 (tp) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 2.1014 time to fit residues: 865.3481 Evaluate side-chains 219 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20556 Z= 0.314 Angle : 0.666 8.277 27884 Z= 0.336 Chirality : 0.039 0.160 3140 Planarity : 0.005 0.062 3440 Dihedral : 5.751 89.511 2720 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.61 % Favored : 95.27 % Rotamer: Outliers : 1.42 % Allowed : 8.73 % Favored : 89.84 % 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: 0.07 (0.17), residues: 2432 helix: 1.34 (0.14), residues: 1428 sheet: -1.75 (0.51), residues: 68 loop : -1.93 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 491 HIS 0.004 0.001 HIS C 246 PHE 0.018 0.002 PHE B 402 TYR 0.017 0.002 TYR D 266 ARG 0.008 0.001 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 281 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8841 (mmp) cc_final: 0.8464 (mmm) REVERT: B 217 GLN cc_start: 0.7248 (mt0) cc_final: 0.6838 (mt0) REVERT: B 334 ARG cc_start: 0.5703 (OUTLIER) cc_final: 0.5188 (mmp-170) REVERT: C 299 LYS cc_start: 0.7903 (tttm) cc_final: 0.7609 (ttmt) REVERT: C 300 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7792 (mm-30) REVERT: D 217 GLN cc_start: 0.7215 (mt0) cc_final: 0.7010 (mt0) outliers start: 31 outliers final: 12 residues processed: 298 average time/residue: 2.2141 time to fit residues: 774.8897 Evaluate side-chains 233 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 220 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 499 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 30.0000 chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 61 optimal weight: 40.0000 chunk 221 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20556 Z= 0.387 Angle : 0.618 7.908 27884 Z= 0.324 Chirality : 0.038 0.159 3140 Planarity : 0.005 0.070 3440 Dihedral : 4.909 58.450 2720 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.93 % Allowed : 12.45 % Favored : 85.62 % 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: -0.15 (0.17), residues: 2432 helix: 1.24 (0.14), residues: 1408 sheet: -1.60 (0.55), residues: 68 loop : -2.12 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 449 HIS 0.004 0.001 HIS D 516 PHE 0.015 0.002 PHE D 204 TYR 0.015 0.002 TYR A 510 ARG 0.007 0.001 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 3.117 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.5234 (mmp) cc_final: 0.4335 (tpp) REVERT: A 346 TRP cc_start: 0.7691 (OUTLIER) cc_final: 0.6742 (t60) REVERT: A 456 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6764 (pp) REVERT: B 117 MET cc_start: 0.5318 (mmp) cc_final: 0.4323 (tpp) REVERT: B 456 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6939 (pp) REVERT: C 117 MET cc_start: 0.5240 (mmp) cc_final: 0.4275 (tpp) REVERT: C 217 GLN cc_start: 0.7810 (mt0) cc_final: 0.7410 (mt0) REVERT: C 250 MET cc_start: 0.8416 (mmt) cc_final: 0.8209 (mmt) REVERT: C 456 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6685 (pp) REVERT: C 626 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8779 (mm) REVERT: D 117 MET cc_start: 0.5332 (mmp) cc_final: 0.4355 (tpp) REVERT: D 346 TRP cc_start: 0.7283 (OUTLIER) cc_final: 0.5744 (t60) REVERT: D 456 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6843 (pp) outliers start: 42 outliers final: 5 residues processed: 238 average time/residue: 1.9610 time to fit residues: 561.3960 Evaluate side-chains 191 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20556 Z= 0.171 Angle : 0.511 5.604 27884 Z= 0.262 Chirality : 0.035 0.132 3140 Planarity : 0.004 0.037 3440 Dihedral : 4.587 49.633 2720 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.88 % Allowed : 14.57 % Favored : 83.55 % 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: 0.32 (0.17), residues: 2432 helix: 1.72 (0.14), residues: 1408 sheet: -1.71 (0.53), residues: 68 loop : -2.07 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 671 HIS 0.003 0.001 HIS C 160 PHE 0.007 0.001 PHE A 596 TYR 0.009 0.001 TYR D 466 ARG 0.003 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 182 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.5332 (mmp) cc_final: 0.4459 (tpp) REVERT: A 375 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8260 (mmtt) REVERT: A 456 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6754 (pp) REVERT: A 602 MET cc_start: 0.8993 (mmp) cc_final: 0.8782 (mmm) REVERT: A 666 MET cc_start: 0.8876 (mtm) cc_final: 0.8527 (mtm) REVERT: B 117 MET cc_start: 0.5302 (mmp) cc_final: 0.4387 (tpp) REVERT: B 360 LYS cc_start: 0.8565 (ptpp) cc_final: 0.7966 (mptt) REVERT: C 117 MET cc_start: 0.5213 (mmp) cc_final: 0.4317 (tpp) REVERT: C 217 GLN cc_start: 0.7733 (mt0) cc_final: 0.7526 (mt0) REVERT: C 250 MET cc_start: 0.8353 (mmt) cc_final: 0.8080 (mmt) REVERT: C 666 MET cc_start: 0.8925 (mtm) cc_final: 0.8630 (mtm) REVERT: D 117 MET cc_start: 0.5313 (mmp) cc_final: 0.4427 (tpp) REVERT: D 346 TRP cc_start: 0.7146 (OUTLIER) cc_final: 0.5735 (t60) outliers start: 41 outliers final: 13 residues processed: 208 average time/residue: 2.0471 time to fit residues: 505.8195 Evaluate side-chains 189 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 30.0000 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 120 optimal weight: 8.9990 chunk 211 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20556 Z= 0.231 Angle : 0.515 7.630 27884 Z= 0.266 Chirality : 0.036 0.129 3140 Planarity : 0.004 0.036 3440 Dihedral : 4.424 53.123 2720 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.16 % Allowed : 14.98 % Favored : 82.86 % 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 (0.17), residues: 2432 helix: 1.83 (0.14), residues: 1404 sheet: -1.81 (0.52), residues: 68 loop : -2.04 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 328 HIS 0.003 0.001 HIS C 160 PHE 0.019 0.001 PHE C 457 TYR 0.011 0.001 TYR B 510 ARG 0.006 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.5389 (mmp) cc_final: 0.4497 (tpp) REVERT: A 375 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8329 (mmtt) REVERT: A 456 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6793 (pp) REVERT: B 117 MET cc_start: 0.5551 (mmp) cc_final: 0.4669 (tpp) REVERT: B 383 ARG cc_start: 0.7698 (tpp80) cc_final: 0.7484 (ttm170) REVERT: B 456 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6891 (pp) REVERT: C 117 MET cc_start: 0.5296 (mmp) cc_final: 0.4413 (tpp) REVERT: D 117 MET cc_start: 0.5452 (mmp) cc_final: 0.4607 (tpp) REVERT: D 346 TRP cc_start: 0.7304 (OUTLIER) cc_final: 0.5977 (t60) REVERT: D 456 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6920 (pp) outliers start: 47 outliers final: 17 residues processed: 202 average time/residue: 2.0594 time to fit residues: 495.2426 Evaluate side-chains 187 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 0.0270 chunk 58 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20556 Z= 0.205 Angle : 0.498 6.295 27884 Z= 0.256 Chirality : 0.035 0.130 3140 Planarity : 0.004 0.038 3440 Dihedral : 4.355 47.792 2720 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.02 % Allowed : 15.67 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2432 helix: 1.96 (0.14), residues: 1400 sheet: -1.89 (0.53), residues: 68 loop : -1.98 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 449 HIS 0.003 0.001 HIS A 246 PHE 0.007 0.001 PHE A 596 TYR 0.008 0.001 TYR B 510 ARG 0.003 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.5452 (mmp) cc_final: 0.4692 (tpp) REVERT: A 375 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8306 (mmtt) REVERT: B 117 MET cc_start: 0.5532 (mmp) cc_final: 0.4704 (tpp) REVERT: B 360 LYS cc_start: 0.8345 (ptpp) cc_final: 0.7861 (mttp) REVERT: C 117 MET cc_start: 0.5461 (mmp) cc_final: 0.4690 (tpp) REVERT: D 117 MET cc_start: 0.5518 (mmp) cc_final: 0.4729 (tpp) REVERT: D 346 TRP cc_start: 0.7365 (OUTLIER) cc_final: 0.6131 (t60) outliers start: 44 outliers final: 18 residues processed: 205 average time/residue: 2.0290 time to fit residues: 496.5697 Evaluate side-chains 191 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20556 Z= 0.360 Angle : 0.567 6.977 27884 Z= 0.297 Chirality : 0.038 0.133 3140 Planarity : 0.004 0.046 3440 Dihedral : 4.610 52.013 2720 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.02 % Allowed : 16.13 % Favored : 81.85 % 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: 0.20 (0.17), residues: 2432 helix: 1.54 (0.14), residues: 1436 sheet: -1.79 (0.52), residues: 68 loop : -2.07 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 328 HIS 0.006 0.001 HIS A 246 PHE 0.013 0.002 PHE C 457 TYR 0.015 0.002 TYR B 510 ARG 0.005 0.001 ARG D 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 180 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.5686 (mmp) cc_final: 0.4997 (tpp) REVERT: A 375 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8429 (mmtt) REVERT: A 456 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6868 (pp) REVERT: B 117 MET cc_start: 0.5700 (mmp) cc_final: 0.5041 (tpp) REVERT: C 117 MET cc_start: 0.5585 (mmp) cc_final: 0.4892 (tpp) REVERT: C 456 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6910 (pp) REVERT: D 117 MET cc_start: 0.5734 (mmp) cc_final: 0.5102 (tpp) REVERT: D 346 TRP cc_start: 0.7745 (OUTLIER) cc_final: 0.6621 (t60) REVERT: D 360 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7850 (mttp) outliers start: 44 outliers final: 23 residues processed: 201 average time/residue: 1.9817 time to fit residues: 477.4455 Evaluate side-chains 195 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 360 LYS Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20556 Z= 0.179 Angle : 0.500 6.540 27884 Z= 0.258 Chirality : 0.035 0.130 3140 Planarity : 0.004 0.040 3440 Dihedral : 4.439 48.719 2720 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.70 % Allowed : 17.42 % Favored : 80.88 % 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: 0.47 (0.17), residues: 2432 helix: 1.81 (0.14), residues: 1432 sheet: -1.87 (0.51), residues: 68 loop : -2.03 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 328 HIS 0.003 0.001 HIS A 246 PHE 0.007 0.001 PHE B 596 TYR 0.008 0.001 TYR D 466 ARG 0.003 0.000 ARG D 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 179 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.5729 (mmp) cc_final: 0.5185 (tpp) REVERT: A 375 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8438 (mmtt) REVERT: A 456 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6966 (pp) REVERT: B 117 MET cc_start: 0.5678 (mmp) cc_final: 0.5166 (tpp) REVERT: C 117 MET cc_start: 0.5586 (mmp) cc_final: 0.5085 (tpp) REVERT: C 441 ILE cc_start: 0.8819 (pt) cc_final: 0.8502 (mt) REVERT: D 117 MET cc_start: 0.5741 (mmp) cc_final: 0.5211 (tpp) REVERT: D 346 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.6515 (t60) outliers start: 37 outliers final: 16 residues processed: 201 average time/residue: 1.9687 time to fit residues: 472.2079 Evaluate side-chains 188 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 205 optimal weight: 0.3980 chunk 219 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 198 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20556 Z= 0.257 Angle : 0.519 8.226 27884 Z= 0.269 Chirality : 0.036 0.127 3140 Planarity : 0.004 0.038 3440 Dihedral : 4.403 48.001 2720 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.61 % Allowed : 17.37 % Favored : 81.02 % 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 (0.17), residues: 2432 helix: 1.82 (0.14), residues: 1432 sheet: -1.80 (0.52), residues: 68 loop : -1.94 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 218 HIS 0.004 0.001 HIS A 246 PHE 0.009 0.001 PHE A 596 TYR 0.014 0.001 TYR C 466 ARG 0.003 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 3.009 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 117 MET cc_start: 0.5754 (mmp) cc_final: 0.5551 (mpp) REVERT: A 375 LYS cc_start: 0.8719 (mmtm) cc_final: 0.8468 (mmtt) REVERT: A 456 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6982 (pp) REVERT: B 117 MET cc_start: 0.5943 (mmp) cc_final: 0.5709 (mpp) REVERT: B 360 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8012 (mttp) REVERT: C 117 MET cc_start: 0.5665 (mmp) cc_final: 0.5401 (mpp) REVERT: C 441 ILE cc_start: 0.8835 (pt) cc_final: 0.8564 (mt) REVERT: D 346 TRP cc_start: 0.7670 (OUTLIER) cc_final: 0.6683 (t60) REVERT: D 441 ILE cc_start: 0.8841 (pt) cc_final: 0.8502 (mt) outliers start: 35 outliers final: 18 residues processed: 206 average time/residue: 1.9986 time to fit residues: 492.8603 Evaluate side-chains 197 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20556 Z= 0.263 Angle : 0.523 7.736 27884 Z= 0.270 Chirality : 0.036 0.127 3140 Planarity : 0.004 0.038 3440 Dihedral : 4.472 49.016 2720 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.33 % Allowed : 18.06 % Favored : 80.61 % 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: 0.53 (0.17), residues: 2432 helix: 1.82 (0.14), residues: 1432 sheet: -1.80 (0.51), residues: 68 loop : -1.93 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 328 HIS 0.005 0.001 HIS A 246 PHE 0.016 0.001 PHE A 204 TYR 0.012 0.001 TYR C 466 ARG 0.003 0.000 ARG A 383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 3.322 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 272 MET cc_start: 0.6847 (mtm) cc_final: 0.6414 (ttm) REVERT: A 375 LYS cc_start: 0.8713 (mmtm) cc_final: 0.8467 (mmtt) REVERT: A 441 ILE cc_start: 0.8832 (pt) cc_final: 0.8609 (mt) REVERT: A 456 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6988 (pp) REVERT: B 360 LYS cc_start: 0.8802 (ptpp) cc_final: 0.8026 (mttp) REVERT: B 441 ILE cc_start: 0.8830 (pt) cc_final: 0.8604 (mt) REVERT: C 441 ILE cc_start: 0.8827 (pt) cc_final: 0.8611 (mt) REVERT: D 441 ILE cc_start: 0.8832 (pt) cc_final: 0.8611 (mt) outliers start: 29 outliers final: 15 residues processed: 203 average time/residue: 2.1262 time to fit residues: 515.0629 Evaluate side-chains 194 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 178 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 199 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.183658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117016 restraints weight = 73544.933| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.49 r_work: 0.3235 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20556 Z= 0.152 Angle : 0.477 7.595 27884 Z= 0.245 Chirality : 0.035 0.127 3140 Planarity : 0.004 0.039 3440 Dihedral : 4.296 46.838 2720 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.87 % Allowed : 18.70 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2432 helix: 2.05 (0.14), residues: 1432 sheet: -1.94 (0.50), residues: 68 loop : -1.83 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 328 HIS 0.003 0.001 HIS C 246 PHE 0.011 0.001 PHE A 204 TYR 0.011 0.001 TYR C 466 ARG 0.003 0.000 ARG A 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11408.91 seconds wall clock time: 201 minutes 25.00 seconds (12085.00 seconds total)