Starting phenix.real_space_refine on Mon Mar 18 03:16:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/03_2024/8dzg_27797_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/03_2024/8dzg_27797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/03_2024/8dzg_27797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/03_2024/8dzg_27797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/03_2024/8dzg_27797_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzg_27797/03_2024/8dzg_27797_updated.pdb" } resolution = 3.1 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= 0.077 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 12 5.49 5 Mg 6 5.21 5 S 84 5.16 5 C 12396 2.51 5 N 3486 2.21 5 O 3768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ASP 330": "OD1" <-> "OD2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C ASP 330": "OD1" <-> "OD2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ASP 341": "OD1" <-> "OD2" Residue "C GLU 522": "OE1" <-> "OE2" Residue "C TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D GLU 522": "OE1" <-> "OE2" Residue "D TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E GLU 318": "OE1" <-> "OE2" Residue "E ASP 330": "OD1" <-> "OD2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ASP 341": "OD1" <-> "OD2" Residue "E GLU 522": "OE1" <-> "OE2" Residue "E TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F ASP 330": "OD1" <-> "OD2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ASP 341": "OD1" <-> "OD2" Residue "F GLU 522": "OE1" <-> "OE2" Residue "F TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19758 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3264 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3264 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3264 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3264 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3264 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3264 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2249 SG CYS A 403 91.228 129.664 31.801 1.00 76.41 S ATOM 2269 SG CYS A 406 94.765 130.815 30.837 1.00 85.65 S ATOM 2553 SG CYS A 445 92.667 132.874 33.325 1.00 94.65 S ATOM 2559 SG CYS A 446 94.089 129.607 34.341 1.00 90.08 S ATOM 5513 SG CYS B 403 31.780 115.896 31.782 1.00 78.66 S ATOM 5533 SG CYS B 406 32.551 119.534 30.816 1.00 88.41 S ATOM 5817 SG CYS B 445 29.718 118.747 33.305 1.00100.25 S ATOM 5823 SG CYS B 446 33.258 118.347 34.321 1.00 95.72 S ATOM 8777 SG CYS C 403 13.977 57.502 31.815 1.00 80.70 S ATOM 8797 SG CYS C 406 11.211 59.989 30.851 1.00 91.67 S ATOM 9081 SG CYS C 445 10.478 57.142 33.339 1.00100.58 S ATOM 9087 SG CYS C 446 12.594 60.007 34.355 1.00 95.77 S ATOM 12041 SG CYS D 403 55.631 12.887 31.802 1.00 76.41 S ATOM 12061 SG CYS D 406 52.094 11.735 30.837 1.00 85.49 S ATOM 12345 SG CYS D 445 54.193 9.677 33.325 1.00 95.67 S ATOM 12351 SG CYS D 446 52.769 12.942 34.341 1.00 91.25 S ATOM 15305 SG CYS E 403 115.103 26.661 31.792 1.00 79.97 S ATOM 15325 SG CYS E 406 114.333 23.022 30.828 1.00 89.12 S ATOM 15609 SG CYS E 445 117.165 23.811 33.316 1.00 99.78 S ATOM 15615 SG CYS E 446 113.625 24.210 34.332 1.00 95.42 S ATOM 18569 SG CYS F 403 132.903 85.057 31.811 1.00 80.23 S ATOM 18589 SG CYS F 406 135.669 82.570 30.849 1.00 91.18 S ATOM 18873 SG CYS F 445 136.401 85.417 33.336 1.00 99.57 S ATOM 18879 SG CYS F 446 134.285 82.552 34.352 1.00 94.82 S Time building chain proxies: 10.11, per 1000 atoms: 0.51 Number of scatterers: 19758 At special positions: 0 Unit cell: (147.96, 143.64, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 84 16.00 P 12 15.00 Mg 6 11.99 O 3768 8.00 N 3486 7.00 C 12396 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: 7.38 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 446 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 445 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 406 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 403 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 446 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 445 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 406 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 403 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 446 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 445 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 406 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 403 " pdb=" ZN D 603 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 446 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 445 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 406 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 403 " pdb=" ZN E 603 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 446 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 445 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 406 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 403 " pdb=" ZN F 603 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 446 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 445 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 406 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 403 " Number of angles added : 36 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 18 sheets defined 38.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 153 through 165 Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 422 through 430 removed outlier: 4.651A pdb=" N GLY A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 521 through 533 Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 153 through 165 Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 422 through 430 removed outlier: 4.651A pdb=" N GLY B 430 " --> pdb=" O LYS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 521 through 533 Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 153 through 165 Processing helix chain 'C' and resid 239 through 250 Processing helix chain 'C' and resid 266 through 280 Processing helix chain 'C' and resid 315 through 328 Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 370 through 377 Processing helix chain 'C' and resid 381 through 385 Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 422 through 430 removed outlier: 4.650A pdb=" N GLY C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 491 through 501 Processing helix chain 'C' and resid 506 through 512 Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 521 through 533 Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 153 through 165 Processing helix chain 'D' and resid 239 through 250 Processing helix chain 'D' and resid 266 through 280 Processing helix chain 'D' and resid 315 through 328 Processing helix chain 'D' and resid 342 through 352 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 410 through 416 Processing helix chain 'D' and resid 422 through 430 removed outlier: 4.651A pdb=" N GLY D 430 " --> pdb=" O LYS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 491 through 501 Processing helix chain 'D' and resid 506 through 512 Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 521 through 533 Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 153 through 165 Processing helix chain 'E' and resid 239 through 250 Processing helix chain 'E' and resid 266 through 280 Processing helix chain 'E' and resid 315 through 328 Processing helix chain 'E' and resid 342 through 352 Processing helix chain 'E' and resid 370 through 377 Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 410 through 416 Processing helix chain 'E' and resid 422 through 430 removed outlier: 4.651A pdb=" N GLY E 430 " --> pdb=" O LYS E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 471 Processing helix chain 'E' and resid 475 through 484 Processing helix chain 'E' and resid 491 through 501 Processing helix chain 'E' and resid 506 through 512 Processing helix chain 'E' and resid 516 through 518 No H-bonds generated for 'chain 'E' and resid 516 through 518' Processing helix chain 'E' and resid 521 through 533 Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 153 through 165 Processing helix chain 'F' and resid 239 through 250 Processing helix chain 'F' and resid 266 through 280 Processing helix chain 'F' and resid 315 through 328 Processing helix chain 'F' and resid 342 through 352 Processing helix chain 'F' and resid 370 through 377 Processing helix chain 'F' and resid 381 through 385 Processing helix chain 'F' and resid 410 through 416 Processing helix chain 'F' and resid 422 through 430 removed outlier: 4.651A pdb=" N GLY F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 471 Processing helix chain 'F' and resid 475 through 484 Processing helix chain 'F' and resid 491 through 501 Processing helix chain 'F' and resid 506 through 512 Processing helix chain 'F' and resid 516 through 518 No H-bonds generated for 'chain 'F' and resid 516 through 518' Processing helix chain 'F' and resid 521 through 533 Processing sheet with id= A, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.892A pdb=" N ASP A 125 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 149 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 139 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU A 147 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS A 141 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N MET A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.645A pdb=" N GLY A 254 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR A 360 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN A 256 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A 362 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 258 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE A 257 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 393 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER A 259 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA A 395 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 287 through 290 removed outlier: 6.296A pdb=" N ILE A 333 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 290 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET A 335 " --> pdb=" O ILE A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 180 through 185 removed outlier: 3.892A pdb=" N ASP B 125 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 149 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 139 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU B 147 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS B 141 " --> pdb=" O MET B 145 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N MET B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.644A pdb=" N GLY B 254 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR B 360 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN B 256 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU B 362 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 258 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 257 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU B 393 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER B 259 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 395 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 287 through 290 removed outlier: 6.297A pdb=" N ILE B 333 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE B 290 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET B 335 " --> pdb=" O ILE B 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 180 through 185 removed outlier: 3.892A pdb=" N ASP C 125 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 149 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 139 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU C 147 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS C 141 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N MET C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.644A pdb=" N GLY C 254 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR C 360 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN C 256 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU C 362 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE C 258 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE C 257 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU C 393 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER C 259 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA C 395 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 287 through 290 removed outlier: 6.297A pdb=" N ILE C 333 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE C 290 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET C 335 " --> pdb=" O ILE C 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.892A pdb=" N ASP D 125 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D 149 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE D 139 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU D 147 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS D 141 " --> pdb=" O MET D 145 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N MET D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.644A pdb=" N GLY D 254 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR D 360 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN D 256 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU D 362 " --> pdb=" O ASN D 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE D 258 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE D 257 " --> pdb=" O THR D 391 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU D 393 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER D 259 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA D 395 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 287 through 290 removed outlier: 6.297A pdb=" N ILE D 333 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE D 290 " --> pdb=" O ILE D 333 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET D 335 " --> pdb=" O ILE D 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 180 through 185 removed outlier: 3.893A pdb=" N ASP E 125 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 149 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE E 139 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU E 147 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS E 141 " --> pdb=" O MET E 145 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N MET E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.644A pdb=" N GLY E 254 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR E 360 " --> pdb=" O GLY E 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN E 256 " --> pdb=" O THR E 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU E 362 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE E 258 " --> pdb=" O LEU E 362 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE E 257 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU E 393 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER E 259 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA E 395 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 287 through 290 removed outlier: 6.297A pdb=" N ILE E 333 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE E 290 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET E 335 " --> pdb=" O ILE E 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 180 through 185 removed outlier: 3.893A pdb=" N ASP F 125 " --> pdb=" O ARG F 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG F 149 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE F 139 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU F 147 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS F 141 " --> pdb=" O MET F 145 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N MET F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 357 through 362 removed outlier: 6.644A pdb=" N GLY F 254 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR F 360 " --> pdb=" O GLY F 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN F 256 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU F 362 " --> pdb=" O ASN F 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE F 258 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE F 257 " --> pdb=" O THR F 391 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU F 393 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER F 259 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA F 395 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 287 through 290 removed outlier: 6.297A pdb=" N ILE F 333 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE F 290 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET F 335 " --> pdb=" O ILE F 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= R 786 hydrogen bonds defined for protein. 2322 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: 5.71 Time building geometry restraints manager: 8.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6624 1.34 - 1.46: 3258 1.46 - 1.58: 10050 1.58 - 1.69: 24 1.69 - 1.81: 132 Bond restraints: 20088 Sorted by residual: bond pdb=" C1' ADP F 602 " pdb=" C2' ADP F 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP D 602 " pdb=" C2' ADP D 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP E 602 " pdb=" C2' ADP E 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP B 602 " pdb=" C2' ADP B 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP A 602 " pdb=" C2' ADP A 602 " ideal model delta sigma weight residual 1.524 1.290 0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 20083 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.44: 638 107.44 - 114.08: 11691 114.08 - 120.71: 8167 120.71 - 127.34: 6534 127.34 - 133.97: 180 Bond angle restraints: 27210 Sorted by residual: angle pdb=" C SER E 170 " pdb=" N ASP E 171 " pdb=" CA ASP E 171 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C SER B 170 " pdb=" N ASP B 171 " pdb=" CA ASP B 171 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C SER C 170 " pdb=" N ASP C 171 " pdb=" CA ASP C 171 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C SER F 170 " pdb=" N ASP F 171 " pdb=" CA ASP F 171 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C SER A 170 " pdb=" N ASP A 171 " pdb=" CA ASP A 171 " ideal model delta sigma weight residual 121.54 130.51 -8.97 1.91e+00 2.74e-01 2.20e+01 ... (remaining 27205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.91: 11774 32.91 - 65.82: 436 65.82 - 98.73: 24 98.73 - 131.64: 6 131.64 - 164.54: 6 Dihedral angle restraints: 12246 sinusoidal: 4914 harmonic: 7332 Sorted by residual: dihedral pdb=" C2' ADP F 602 " pdb=" C1' ADP F 602 " pdb=" N9 ADP F 602 " pdb=" C4 ADP F 602 " ideal model delta sinusoidal sigma weight residual 91.55 -73.00 164.54 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C2' ADP E 602 " pdb=" C1' ADP E 602 " pdb=" N9 ADP E 602 " pdb=" C4 ADP E 602 " ideal model delta sinusoidal sigma weight residual 91.55 -72.99 164.53 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C2' ADP C 602 " pdb=" C1' ADP C 602 " pdb=" N9 ADP C 602 " pdb=" C4 ADP C 602 " ideal model delta sinusoidal sigma weight residual 91.55 -72.98 164.52 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 12243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1790 0.027 - 0.055: 758 0.055 - 0.082: 320 0.082 - 0.110: 133 0.110 - 0.137: 119 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA ILE E 258 " pdb=" N ILE E 258 " pdb=" C ILE E 258 " pdb=" CB ILE E 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE A 258 " pdb=" N ILE A 258 " pdb=" C ILE A 258 " pdb=" CB ILE A 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 3117 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 526 " -0.012 2.00e-02 2.50e+03 1.55e-02 4.82e+00 pdb=" CG TYR F 526 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR F 526 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR F 526 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR F 526 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 526 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 526 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 526 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 193 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 194 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 194 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 194 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 526 " -0.011 2.00e-02 2.50e+03 1.54e-02 4.74e+00 pdb=" CG TYR E 526 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 526 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR E 526 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR E 526 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 526 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 526 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 526 " 0.001 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 174 2.64 - 3.21: 16639 3.21 - 3.77: 29108 3.77 - 4.34: 40074 4.34 - 4.90: 68423 Nonbonded interactions: 154418 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O2B ADP D 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ADP C 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG A 601 " pdb=" O2B ADP A 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2B ADP B 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG E 601 " pdb=" O2B ADP E 602 " model vdw 2.076 2.170 ... (remaining 154413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 4.770 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 55.900 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.008 0.235 20088 Z= 0.499 Angle : 0.733 11.913 27210 Z= 0.355 Chirality : 0.044 0.137 3120 Planarity : 0.005 0.054 3486 Dihedral : 16.805 164.544 7506 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.29 % Allowed : 12.39 % Favored : 87.32 % 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 (0.16), residues: 2496 helix: 0.78 (0.15), residues: 1104 sheet: 1.42 (0.21), residues: 546 loop : -2.41 (0.17), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 359 HIS 0.004 0.001 HIS E 127 PHE 0.010 0.001 PHE D 382 TYR 0.038 0.001 TYR F 526 ARG 0.002 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 2.219 Fit side-chains REVERT: A 463 ASP cc_start: 0.7240 (m-30) cc_final: 0.6944 (m-30) REVERT: C 338 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: C 489 MET cc_start: 0.8396 (ttp) cc_final: 0.8130 (ttp) REVERT: D 463 ASP cc_start: 0.7313 (m-30) cc_final: 0.6964 (m-30) REVERT: F 489 MET cc_start: 0.8395 (ttp) cc_final: 0.8134 (ttp) outliers start: 6 outliers final: 0 residues processed: 161 average time/residue: 0.3447 time to fit residues: 84.0887 Evaluate side-chains 137 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 147 optimal weight: 0.0870 chunk 228 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 205 ASN A 363 HIS B 205 ASN B 363 HIS C 205 ASN D 166 ASN D 205 ASN D 363 HIS ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 ASN E 363 HIS F 205 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20088 Z= 0.156 Angle : 0.517 6.746 27210 Z= 0.249 Chirality : 0.041 0.134 3120 Planarity : 0.004 0.047 3486 Dihedral : 10.400 160.951 2823 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.69 % Favored : 95.07 % Rotamer: Outliers : 1.73 % Allowed : 12.63 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2496 helix: 1.52 (0.16), residues: 1104 sheet: 1.59 (0.21), residues: 546 loop : -2.38 (0.17), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 359 HIS 0.002 0.001 HIS C 239 PHE 0.009 0.001 PHE F 204 TYR 0.019 0.001 TYR F 526 ARG 0.001 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 2.462 Fit side-chains REVERT: A 463 ASP cc_start: 0.7168 (m-30) cc_final: 0.6710 (m-30) REVERT: A 526 TYR cc_start: 0.7855 (t80) cc_final: 0.7513 (t80) REVERT: B 166 ASN cc_start: 0.7784 (m-40) cc_final: 0.7498 (m-40) REVERT: C 489 MET cc_start: 0.8367 (ttp) cc_final: 0.8094 (ttp) REVERT: D 463 ASP cc_start: 0.7203 (m-30) cc_final: 0.6745 (m-30) REVERT: D 526 TYR cc_start: 0.7899 (t80) cc_final: 0.7521 (t80) REVERT: E 166 ASN cc_start: 0.7797 (m-40) cc_final: 0.7527 (m-40) REVERT: F 489 MET cc_start: 0.8362 (ttp) cc_final: 0.8100 (ttp) outliers start: 36 outliers final: 21 residues processed: 179 average time/residue: 0.3138 time to fit residues: 88.3344 Evaluate side-chains 162 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain F residue 420 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 20088 Z= 0.568 Angle : 0.753 9.392 27210 Z= 0.377 Chirality : 0.052 0.180 3120 Planarity : 0.006 0.092 3486 Dihedral : 10.964 163.224 2820 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.37 % Favored : 93.39 % Rotamer: Outliers : 3.70 % Allowed : 12.87 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.44 % 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: -0.22 (0.16), residues: 2496 helix: 1.10 (0.16), residues: 1092 sheet: 0.72 (0.20), residues: 546 loop : -2.46 (0.17), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 359 HIS 0.005 0.001 HIS B 127 PHE 0.015 0.002 PHE B 204 TYR 0.015 0.002 TYR B 526 ARG 0.004 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 162 time to evaluate : 2.161 Fit side-chains REVERT: A 338 GLU cc_start: 0.8080 (tt0) cc_final: 0.7854 (tt0) REVERT: A 346 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6771 (m110) REVERT: A 463 ASP cc_start: 0.7563 (m-30) cc_final: 0.7219 (m-30) REVERT: A 526 TYR cc_start: 0.8016 (t80) cc_final: 0.7575 (t80) REVERT: B 262 THR cc_start: 0.8964 (t) cc_final: 0.8679 (t) REVERT: C 166 ASN cc_start: 0.7872 (m110) cc_final: 0.7589 (m110) REVERT: C 318 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: C 450 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: C 507 MET cc_start: 0.7270 (mpp) cc_final: 0.7049 (mpp) REVERT: D 279 ILE cc_start: 0.8457 (mm) cc_final: 0.8248 (mt) REVERT: D 463 ASP cc_start: 0.7555 (m-30) cc_final: 0.7213 (m-30) REVERT: D 526 TYR cc_start: 0.8010 (t80) cc_final: 0.7570 (t80) REVERT: E 262 THR cc_start: 0.8960 (t) cc_final: 0.8673 (t) REVERT: F 166 ASN cc_start: 0.7831 (m110) cc_final: 0.7564 (m110) REVERT: F 318 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: F 450 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: F 507 MET cc_start: 0.7271 (mpp) cc_final: 0.7066 (mpp) outliers start: 77 outliers final: 61 residues processed: 220 average time/residue: 0.2824 time to fit residues: 100.2565 Evaluate side-chains 213 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 147 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 500 ILE Chi-restraints excluded: chain E residue 501 SER Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 450 TYR Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 153 optimal weight: 0.0270 chunk 230 optimal weight: 0.7980 chunk 243 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20088 Z= 0.160 Angle : 0.526 7.561 27210 Z= 0.260 Chirality : 0.042 0.136 3120 Planarity : 0.005 0.083 3486 Dihedral : 9.838 154.063 2820 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 2.11 % Allowed : 16.23 % Favored : 81.65 % 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: 0.30 (0.17), residues: 2496 helix: 1.73 (0.16), residues: 1104 sheet: 1.18 (0.20), residues: 546 loop : -2.73 (0.17), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 359 HIS 0.004 0.001 HIS D 127 PHE 0.008 0.001 PHE B 382 TYR 0.014 0.001 TYR E 526 ARG 0.001 0.000 ARG F 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 149 time to evaluate : 2.435 Fit side-chains REVERT: A 338 GLU cc_start: 0.8007 (tt0) cc_final: 0.7785 (tt0) REVERT: A 463 ASP cc_start: 0.7414 (m-30) cc_final: 0.6961 (m-30) REVERT: A 526 TYR cc_start: 0.7887 (t80) cc_final: 0.7397 (t80) REVERT: B 262 THR cc_start: 0.8841 (t) cc_final: 0.8562 (t) REVERT: C 166 ASN cc_start: 0.7845 (m110) cc_final: 0.7480 (m110) REVERT: C 507 MET cc_start: 0.7140 (mpp) cc_final: 0.6904 (mpp) REVERT: D 346 ASN cc_start: 0.7069 (OUTLIER) cc_final: 0.6710 (m110) REVERT: D 463 ASP cc_start: 0.7444 (m-30) cc_final: 0.7000 (m-30) REVERT: D 526 TYR cc_start: 0.7908 (t80) cc_final: 0.7421 (t80) REVERT: E 262 THR cc_start: 0.8846 (t) cc_final: 0.8564 (t) REVERT: F 166 ASN cc_start: 0.7885 (m110) cc_final: 0.7530 (m110) REVERT: F 507 MET cc_start: 0.7139 (mpp) cc_final: 0.6909 (mpp) outliers start: 44 outliers final: 33 residues processed: 178 average time/residue: 0.3117 time to fit residues: 89.0683 Evaluate side-chains 179 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20088 Z= 0.221 Angle : 0.557 8.453 27210 Z= 0.277 Chirality : 0.043 0.139 3120 Planarity : 0.005 0.079 3486 Dihedral : 9.690 152.725 2820 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.77 % Favored : 93.99 % Rotamer: Outliers : 2.45 % Allowed : 16.47 % Favored : 81.08 % 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: 2496 helix: 1.77 (0.16), residues: 1110 sheet: 1.16 (0.21), residues: 546 loop : -2.77 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.003 0.001 HIS B 127 PHE 0.009 0.001 PHE F 204 TYR 0.016 0.001 TYR F 526 ARG 0.002 0.000 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 149 time to evaluate : 2.250 Fit side-chains REVERT: A 338 GLU cc_start: 0.8037 (tt0) cc_final: 0.7830 (tt0) REVERT: A 463 ASP cc_start: 0.7447 (m-30) cc_final: 0.6981 (m-30) REVERT: A 526 TYR cc_start: 0.7915 (t80) cc_final: 0.7421 (t80) REVERT: B 262 THR cc_start: 0.8840 (t) cc_final: 0.8548 (t) REVERT: B 500 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8035 (mp) REVERT: C 507 MET cc_start: 0.7221 (mpp) cc_final: 0.6955 (mpp) REVERT: D 346 ASN cc_start: 0.7088 (OUTLIER) cc_final: 0.6734 (m110) REVERT: D 463 ASP cc_start: 0.7392 (m-30) cc_final: 0.6924 (m-30) REVERT: D 526 TYR cc_start: 0.7916 (t80) cc_final: 0.7430 (t80) REVERT: E 262 THR cc_start: 0.8839 (t) cc_final: 0.8543 (t) REVERT: E 500 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8031 (mp) REVERT: F 507 MET cc_start: 0.7224 (mpp) cc_final: 0.6962 (mpp) outliers start: 51 outliers final: 41 residues processed: 186 average time/residue: 0.2836 time to fit residues: 84.5131 Evaluate side-chains 191 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 500 ILE Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 143 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 243 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20088 Z= 0.183 Angle : 0.532 7.223 27210 Z= 0.264 Chirality : 0.042 0.134 3120 Planarity : 0.004 0.062 3486 Dihedral : 9.399 148.985 2820 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.01 % Favored : 93.75 % Rotamer: Outliers : 2.50 % Allowed : 17.15 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2496 helix: 1.92 (0.16), residues: 1110 sheet: 1.29 (0.21), residues: 546 loop : -2.72 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.003 0.001 HIS A 127 PHE 0.008 0.001 PHE C 204 TYR 0.016 0.001 TYR E 526 ARG 0.001 0.000 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 152 time to evaluate : 2.079 Fit side-chains REVERT: A 338 GLU cc_start: 0.8019 (tt0) cc_final: 0.7809 (tt0) REVERT: A 463 ASP cc_start: 0.7347 (m-30) cc_final: 0.6867 (m-30) REVERT: A 526 TYR cc_start: 0.7916 (t80) cc_final: 0.7440 (t80) REVERT: B 163 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 262 THR cc_start: 0.8822 (t) cc_final: 0.8541 (t) REVERT: B 500 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 507 MET cc_start: 0.7194 (mpp) cc_final: 0.6929 (mpp) REVERT: C 526 TYR cc_start: 0.7914 (t80) cc_final: 0.7597 (t80) REVERT: D 346 ASN cc_start: 0.7104 (OUTLIER) cc_final: 0.6747 (m110) REVERT: D 463 ASP cc_start: 0.7336 (m-30) cc_final: 0.6858 (m-30) REVERT: D 526 TYR cc_start: 0.7893 (t80) cc_final: 0.7416 (t80) REVERT: E 262 THR cc_start: 0.8830 (t) cc_final: 0.8544 (t) REVERT: F 507 MET cc_start: 0.7195 (mpp) cc_final: 0.6935 (mpp) REVERT: F 526 TYR cc_start: 0.7917 (t80) cc_final: 0.7598 (t80) outliers start: 52 outliers final: 42 residues processed: 189 average time/residue: 0.2800 time to fit residues: 85.5105 Evaluate side-chains 194 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 205 optimal weight: 0.0370 chunk 136 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 148 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20088 Z= 0.175 Angle : 0.528 6.396 27210 Z= 0.261 Chirality : 0.042 0.133 3120 Planarity : 0.004 0.063 3486 Dihedral : 9.169 146.906 2820 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.57 % Favored : 94.19 % Rotamer: Outliers : 2.50 % Allowed : 17.96 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2496 helix: 2.00 (0.16), residues: 1110 sheet: 1.26 (0.21), residues: 552 loop : -2.69 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.003 0.001 HIS A 127 PHE 0.008 0.001 PHE F 382 TYR 0.017 0.001 TYR E 526 ARG 0.001 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 159 time to evaluate : 2.272 Fit side-chains REVERT: A 338 GLU cc_start: 0.8033 (tt0) cc_final: 0.7832 (tt0) REVERT: A 463 ASP cc_start: 0.7312 (m-30) cc_final: 0.6837 (m-30) REVERT: A 526 TYR cc_start: 0.7925 (t80) cc_final: 0.7449 (t80) REVERT: B 163 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 262 THR cc_start: 0.8815 (t) cc_final: 0.8539 (t) REVERT: C 340 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7634 (ptp-170) REVERT: C 507 MET cc_start: 0.7180 (mpp) cc_final: 0.6919 (mpp) REVERT: C 526 TYR cc_start: 0.7935 (t80) cc_final: 0.7694 (t80) REVERT: D 346 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6756 (m110) REVERT: D 463 ASP cc_start: 0.7278 (m-30) cc_final: 0.6804 (m-30) REVERT: D 526 TYR cc_start: 0.7926 (t80) cc_final: 0.7448 (t80) REVERT: E 262 THR cc_start: 0.8828 (t) cc_final: 0.8542 (t) REVERT: F 340 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7583 (ptp-170) REVERT: F 507 MET cc_start: 0.7197 (mpp) cc_final: 0.6928 (mpp) REVERT: F 526 TYR cc_start: 0.7938 (t80) cc_final: 0.7695 (t80) outliers start: 52 outliers final: 42 residues processed: 198 average time/residue: 0.3156 time to fit residues: 97.3811 Evaluate side-chains 202 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 156 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.0670 chunk 96 optimal weight: 3.9990 chunk 145 optimal weight: 0.0870 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 190 optimal weight: 4.9990 chunk 220 optimal weight: 0.0050 overall best weight: 0.3110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN C 180 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN F 180 GLN ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 20088 Z= 0.136 Angle : 0.510 6.078 27210 Z= 0.251 Chirality : 0.041 0.158 3120 Planarity : 0.004 0.053 3486 Dihedral : 8.683 139.587 2820 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.41 % Favored : 94.35 % Rotamer: Outliers : 1.97 % Allowed : 18.78 % Favored : 79.25 % 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: 0.80 (0.17), residues: 2496 helix: 2.13 (0.16), residues: 1110 sheet: 1.49 (0.21), residues: 552 loop : -2.56 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.004 0.000 HIS F 157 PHE 0.008 0.001 PHE F 382 TYR 0.017 0.001 TYR E 526 ARG 0.001 0.000 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 2.108 Fit side-chains REVERT: A 338 GLU cc_start: 0.7987 (tt0) cc_final: 0.7782 (tt0) REVERT: A 463 ASP cc_start: 0.7189 (m-30) cc_final: 0.6696 (m-30) REVERT: A 526 TYR cc_start: 0.7887 (t80) cc_final: 0.7494 (t80) REVERT: B 163 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7912 (mp) REVERT: B 262 THR cc_start: 0.8808 (t) cc_final: 0.8546 (t) REVERT: C 340 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7551 (ptp-170) REVERT: C 507 MET cc_start: 0.7071 (mpp) cc_final: 0.6812 (mpp) REVERT: D 346 ASN cc_start: 0.7091 (OUTLIER) cc_final: 0.6749 (m110) REVERT: D 463 ASP cc_start: 0.7171 (m-30) cc_final: 0.6683 (m-30) REVERT: D 526 TYR cc_start: 0.7889 (t80) cc_final: 0.7493 (t80) REVERT: E 262 THR cc_start: 0.8792 (t) cc_final: 0.8523 (t) REVERT: F 340 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7537 (ptp-170) REVERT: F 507 MET cc_start: 0.7070 (mpp) cc_final: 0.6819 (mpp) outliers start: 41 outliers final: 27 residues processed: 187 average time/residue: 0.3041 time to fit residues: 90.8164 Evaluate side-chains 188 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 420 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 225 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN B 180 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20088 Z= 0.269 Angle : 0.578 7.424 27210 Z= 0.288 Chirality : 0.044 0.146 3120 Planarity : 0.004 0.060 3486 Dihedral : 9.220 150.293 2820 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.89 % Favored : 93.79 % Rotamer: Outliers : 2.16 % Allowed : 18.78 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2496 helix: 1.90 (0.16), residues: 1110 sheet: 1.27 (0.21), residues: 546 loop : -2.79 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 359 HIS 0.007 0.001 HIS A 127 PHE 0.011 0.001 PHE F 204 TYR 0.029 0.001 TYR F 526 ARG 0.002 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 158 time to evaluate : 2.470 Fit side-chains REVERT: A 338 GLU cc_start: 0.8039 (tt0) cc_final: 0.7833 (tt0) REVERT: A 463 ASP cc_start: 0.7305 (m-30) cc_final: 0.6855 (m-30) REVERT: A 526 TYR cc_start: 0.7963 (t80) cc_final: 0.7507 (t80) REVERT: B 262 THR cc_start: 0.8908 (t) cc_final: 0.8605 (t) REVERT: C 340 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7642 (ptp-170) REVERT: C 450 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: C 507 MET cc_start: 0.7293 (mpp) cc_final: 0.7016 (mpp) REVERT: D 346 ASN cc_start: 0.7148 (OUTLIER) cc_final: 0.6763 (m110) REVERT: D 463 ASP cc_start: 0.7301 (m-30) cc_final: 0.6853 (m-30) REVERT: D 526 TYR cc_start: 0.7951 (t80) cc_final: 0.7508 (t80) REVERT: E 262 THR cc_start: 0.8913 (t) cc_final: 0.8607 (t) REVERT: F 450 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: F 507 MET cc_start: 0.7275 (mpp) cc_final: 0.7022 (mpp) outliers start: 45 outliers final: 35 residues processed: 190 average time/residue: 0.2862 time to fit residues: 87.1706 Evaluate side-chains 193 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 154 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 450 TYR Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN F 303 GLN F 439 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 20088 Z= 0.323 Angle : 0.613 7.680 27210 Z= 0.306 Chirality : 0.045 0.149 3120 Planarity : 0.005 0.060 3486 Dihedral : 9.501 152.927 2820 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.53 % Favored : 93.07 % Rotamer: Outliers : 2.21 % Allowed : 19.12 % Favored : 78.67 % 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: 0.16 (0.17), residues: 2496 helix: 1.68 (0.16), residues: 1110 sheet: 1.01 (0.21), residues: 546 loop : -2.87 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.004 0.001 HIS F 239 PHE 0.012 0.002 PHE C 204 TYR 0.029 0.001 TYR F 526 ARG 0.002 0.000 ARG D 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 151 time to evaluate : 2.385 Fit side-chains REVERT: A 338 GLU cc_start: 0.8122 (tt0) cc_final: 0.7901 (tt0) REVERT: A 463 ASP cc_start: 0.7522 (m-30) cc_final: 0.7059 (m-30) REVERT: A 526 TYR cc_start: 0.7980 (t80) cc_final: 0.7529 (t80) REVERT: B 262 THR cc_start: 0.8971 (t) cc_final: 0.8638 (t) REVERT: C 340 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7682 (ptp-170) REVERT: C 450 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: C 507 MET cc_start: 0.7244 (mpp) cc_final: 0.6963 (mpp) REVERT: D 346 ASN cc_start: 0.7110 (OUTLIER) cc_final: 0.6744 (m110) REVERT: D 463 ASP cc_start: 0.7538 (m-30) cc_final: 0.7077 (m-30) REVERT: D 526 TYR cc_start: 0.7974 (t80) cc_final: 0.7529 (t80) REVERT: E 262 THR cc_start: 0.8972 (t) cc_final: 0.8635 (t) REVERT: F 507 MET cc_start: 0.7325 (mpp) cc_final: 0.7056 (mpp) outliers start: 46 outliers final: 39 residues processed: 186 average time/residue: 0.3020 time to fit residues: 89.6602 Evaluate side-chains 186 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 303 GLN Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.143023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109331 restraints weight = 21006.025| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.89 r_work: 0.2975 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20088 Z= 0.199 Angle : 0.551 6.696 27210 Z= 0.275 Chirality : 0.042 0.146 3120 Planarity : 0.004 0.058 3486 Dihedral : 9.116 149.535 2820 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.97 % Favored : 93.63 % Rotamer: Outliers : 2.07 % Allowed : 19.64 % Favored : 78.29 % 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: 0.36 (0.17), residues: 2496 helix: 1.84 (0.16), residues: 1110 sheet: 1.19 (0.21), residues: 546 loop : -2.81 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.003 0.001 HIS E 127 PHE 0.007 0.001 PHE C 382 TYR 0.030 0.001 TYR F 526 ARG 0.001 0.000 ARG C 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.89 seconds wall clock time: 67 minutes 50.63 seconds (4070.63 seconds total)