Starting phenix.real_space_refine on Wed Jul 24 15:02:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqi_41505/07_2024/8tqi_41505.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqi_41505/07_2024/8tqi_41505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqi_41505/07_2024/8tqi_41505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqi_41505/07_2024/8tqi_41505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqi_41505/07_2024/8tqi_41505.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqi_41505/07_2024/8tqi_41505.cif" } resolution = 3.24 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= 0.026 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2635 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 71 5.16 5 C 7940 2.51 5 N 2080 2.21 5 O 2437 1.98 5 H 11831 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "L ASP 30": "OD1" <-> "OD2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24359 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6344 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 395} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 6349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 6349 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 393} Chain breaks: 3 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1548 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU%NH3:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1543 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1444 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1143 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain breaks: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1687 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU%NH3:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1636 Classifications: {'peptide': 111} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1625 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1040 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 10.92, per 1000 atoms: 0.45 Number of scatterers: 24359 At special positions: 0 Unit cell: (110.2, 118.75, 112.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 O 2437 8.00 N 2080 7.00 C 7940 6.00 H 11831 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 269 " distance=2.01 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 363 " distance=1.98 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 469 " distance=2.04 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 473 " distance=2.05 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 256 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 363 " distance=2.88 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 469 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 473 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 544 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 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: 16.64 Conformation dependent library (CDL) restraints added in 2.6 seconds 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3062 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 35 sheets defined 4.6% alpha, 39.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 275 through 280 removed outlier: 3.650A pdb=" N TYR B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.589A pdb=" N ILE B 309 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 368 No H-bonds generated for 'chain 'B' and resid 367 through 368' Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.867A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.854A pdb=" N ILE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.899A pdb=" N ALA A 528 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 551 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR A 530 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 179 Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 198 removed outlier: 6.638A pdb=" N THR A 206 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 196 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 204 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLN A 222 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR A 246 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 224 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER A 244 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 226 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 228 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 254 through 261 removed outlier: 5.417A pdb=" N SER A 255 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A 270 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.866A pdb=" N SER A 310 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 396 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 332 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU A 335 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR A 337 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A 318 " --> pdb=" O TYR A 337 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY A 339 " --> pdb=" O ALA A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.866A pdb=" N SER A 310 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 396 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 332 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 410 through 414 removed outlier: 4.529A pdb=" N ILE A 419 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 481 through 483 Processing sheet with id=AB2, first strand: chain 'B' and resid 148 through 150 removed outlier: 6.681A pdb=" N ALA B 528 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 551 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR B 530 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AB4, first strand: chain 'B' and resid 190 through 198 removed outlier: 5.626A pdb=" N VAL B 191 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 210 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR B 193 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN B 208 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN B 222 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR B 246 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 224 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER B 244 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 226 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 254 through 261 removed outlier: 5.259A pdb=" N SER B 255 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B 270 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 310 through 311 removed outlier: 6.831A pdb=" N SER B 310 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR B 398 " --> pdb=" O SER B 310 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 332 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 310 through 311 removed outlier: 6.831A pdb=" N SER B 310 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR B 398 " --> pdb=" O SER B 310 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 332 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 410 through 415 removed outlier: 4.616A pdb=" N ILE B 419 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN B 433 " --> pdb=" O THR B 423 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 481 through 483 Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.551A pdb=" N LEU C 80 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.963A pdb=" N ALA D 84 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'E' and resid 57 through 58 removed outlier: 5.251A pdb=" N CYS E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG E 38 " --> pdb=" O CYS E 47 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.952A pdb=" N THR F 5 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG F 24 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.408A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN F 90 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR F 96 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.563A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.384A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.384A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'I' and resid 57 through 58 removed outlier: 5.382A pdb=" N CYS I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG I 38 " --> pdb=" O CYS I 47 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 22 through 24 Processing sheet with id=AD8, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.600A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1170 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: 9.02 Time building geometry restraints manager: 17.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11829 1.04 - 1.24: 1683 1.24 - 1.44: 3973 1.44 - 1.64: 7065 1.64 - 1.84: 98 Bond restraints: 24648 Sorted by residual: bond pdb=" N PRO A 470 " pdb=" CA PRO A 470 " ideal model delta sigma weight residual 1.469 1.695 -0.226 1.28e-02 6.10e+03 3.12e+02 bond pdb=" C THR A 193 " pdb=" N PRO A 194 " ideal model delta sigma weight residual 1.331 1.539 -0.208 1.28e-02 6.10e+03 2.64e+02 bond pdb=" N PRO A 568 " pdb=" CA PRO A 568 " ideal model delta sigma weight residual 1.479 1.690 -0.211 1.56e-02 4.11e+03 1.83e+02 bond pdb=" C ILE A 567 " pdb=" N PRO A 568 " ideal model delta sigma weight residual 1.334 1.455 -0.121 2.34e-02 1.83e+03 2.69e+01 bond pdb=" C CYS A 469 " pdb=" N PRO A 470 " ideal model delta sigma weight residual 1.334 1.442 -0.108 2.34e-02 1.83e+03 2.13e+01 ... (remaining 24643 not shown) Histogram of bond angle deviations from ideal: 100.00 - 107.58: 1432 107.58 - 115.16: 29327 115.16 - 122.74: 9626 122.74 - 130.33: 3837 130.33 - 137.91: 68 Bond angle restraints: 44290 Sorted by residual: angle pdb=" C CYS A 469 " pdb=" N PRO A 470 " pdb=" CA PRO A 470 " ideal model delta sigma weight residual 119.84 137.74 -17.90 1.25e+00 6.40e-01 2.05e+02 angle pdb=" C THR A 193 " pdb=" N PRO A 194 " pdb=" CA PRO A 194 " ideal model delta sigma weight residual 119.99 131.31 -11.32 1.08e+00 8.57e-01 1.10e+02 angle pdb=" CA PRO A 568 " pdb=" N PRO A 568 " pdb=" CD PRO A 568 " ideal model delta sigma weight residual 112.00 100.06 11.94 1.40e+00 5.10e-01 7.28e+01 angle pdb=" N GLN D 37 " pdb=" CA GLN D 37 " pdb=" C GLN D 37 " ideal model delta sigma weight residual 109.07 120.27 -11.20 1.61e+00 3.86e-01 4.84e+01 angle pdb=" C ILE A 567 " pdb=" N PRO A 568 " pdb=" CA PRO A 568 " ideal model delta sigma weight residual 120.25 137.91 -17.66 2.57e+00 1.51e-01 4.72e+01 ... (remaining 44285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 10436 17.05 - 34.09: 994 34.09 - 51.14: 358 51.14 - 68.19: 98 68.19 - 85.23: 13 Dihedral angle restraints: 11899 sinusoidal: 6243 harmonic: 5656 Sorted by residual: dihedral pdb=" CB CYS A 159 " pdb=" SG CYS A 159 " pdb=" SG CYS A 571 " pdb=" CB CYS A 571 " ideal model delta sinusoidal sigma weight residual -86.00 -168.89 82.89 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS B 350 " pdb=" SG CYS B 350 " pdb=" SG CYS B 363 " pdb=" CB CYS B 363 " ideal model delta sinusoidal sigma weight residual -86.00 -158.70 72.70 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS B 190 " pdb=" SG CYS B 190 " pdb=" SG CYS B 214 " pdb=" CB CYS B 214 " ideal model delta sinusoidal sigma weight residual 93.00 157.28 -64.28 1 1.00e+01 1.00e-02 5.43e+01 ... (remaining 11896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1873 0.108 - 0.217: 123 0.217 - 0.325: 5 0.325 - 0.433: 0 0.433 - 0.542: 1 Chirality restraints: 2002 Sorted by residual: chirality pdb=" CA PRO A 470 " pdb=" N PRO A 470 " pdb=" C PRO A 470 " pdb=" CB PRO A 470 " both_signs ideal model delta sigma weight residual False 2.72 3.26 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA PRO A 568 " pdb=" N PRO A 568 " pdb=" C PRO A 568 " pdb=" CB PRO A 568 " both_signs ideal model delta sigma weight residual False 2.72 3.04 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA THR A 353 " pdb=" N THR A 353 " pdb=" C THR A 353 " pdb=" CB THR A 353 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1999 not shown) Planarity restraints: 3764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 460 " -0.217 2.00e-02 2.50e+03 2.49e-01 9.28e+02 pdb=" CG ASN A 460 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 460 " 0.210 2.00e-02 2.50e+03 pdb=" ND2 ASN A 460 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 460 " -0.378 2.00e-02 2.50e+03 pdb="HD22 ASN A 460 " 0.370 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 240 " -0.160 2.00e-02 2.50e+03 1.71e-01 4.40e+02 pdb=" CG ASN B 240 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 240 " 0.149 2.00e-02 2.50e+03 pdb=" ND2 ASN B 240 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 240 " 0.249 2.00e-02 2.50e+03 pdb="HD22 ASN B 240 " -0.257 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 93 " 0.095 2.00e-02 2.50e+03 1.00e-01 1.51e+02 pdb=" CG ASN F 93 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN F 93 " -0.090 2.00e-02 2.50e+03 pdb=" ND2 ASN F 93 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN F 93 " 0.149 2.00e-02 2.50e+03 pdb="HD22 ASN F 93 " -0.145 2.00e-02 2.50e+03 ... (remaining 3761 not shown) Histogram of nonbonded interaction distances: 1.34 - 1.99: 123 1.99 - 2.65: 31181 2.65 - 3.30: 64631 3.30 - 3.95: 87679 3.95 - 4.60: 137756 Nonbonded interactions: 321370 Sorted by model distance: nonbonded pdb=" SG CYS B 350 " pdb=" HB3 CYS B 363 " model vdw 1.343 2.416 nonbonded pdb="HG23 THR A 193 " pdb="HG11 VAL A 322 " model vdw 1.397 2.440 nonbonded pdb=" HB3 PRO B 370 " pdb=" OD2 ASP E 31 " model vdw 1.420 2.620 nonbonded pdb="HG21 THR A 193 " pdb="HG11 VAL A 322 " model vdw 1.478 2.440 nonbonded pdb=" HG3 PRO B 370 " pdb=" OD1 ASP E 31 " model vdw 1.510 2.620 ... (remaining 321365 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' and (resid 142 through 153 or (resid 154 through 155 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 156 throu \ gh 232 or (resid 235 and (name N or name CA or name C or name O or name CB or na \ me HA )) or resid 236 through 272 or (resid 273 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 274 through 275 or (resid \ 276 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 277 through 294 or (resid 295 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 296 through 385 or resid 391 th \ rough 394 or (resid 395 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 396 through 571)) selection = (chain 'B' and (resid 142 through 144 or (resid 145 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 146 through 159 or re \ sid 164 through 250 or (resid 251 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 252 through 344 or (resid 345 through 3 \ 46 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 347 through 384 or (resid 385 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 391 through 401 or (resid 402 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 403 through 445 or (resid 446 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 447 through 461 or (resid 462 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 46 \ 3 through 552 or (resid 553 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 554 through 571)) } ncs_group { reference = (chain 'C' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 62 through 74 or (resid 7 \ 5 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 76 through 82 or (resid 82A and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2 or name H or name HA )) or resid 8 \ 2B through 84 or (resid 85 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 86 through 103)) selection = (chain 'H' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 4 through 12 or (resid 13 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 14 through 15 or (resid 16 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 17 through 18 or (resid 19 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 20 thr \ ough 103)) } ncs_group { reference = (chain 'D' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA )) or resid 71 through 106)) selection = (chain 'L' and (resid 1 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 43 through 80 or (resid 8 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 82 through 102 or (resid 103 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 104 or (resid 105 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 106)) } ncs_group { reference = (chain 'E' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 6 through 71 or resid 76 th \ rough 103 or (resid 104 and (name N or name CA or name C or name O )))) selection = (chain 'I' and (resid 2 through 7 or (resid 18 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 o \ r name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or nam \ e HD22 or name HD23)) or resid 19 through 31 or (resid 32 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 33 through 39 o \ r (resid 40 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 41 through 42 or (resid 45 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or \ name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name \ HD22 or name HD23)) or resid 46 through 63 or (resid 64 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 65 through 66 or \ (resid 67 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 68 through 71 or (resid 76 and (name N or name CA or name C or \ name O or name CB or name HA )) or (resid 77 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 78 through 80 or (resid 81 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ (resid 87 and (name N or name CA or name C or name O or name CB or name OG1 or \ name CG2 or name HA or name HB or name HG1 or name HG21 or name HG22 or name HG2 \ 3)) or resid 88 through 104)) } 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.410 Extract box with map and model: 0.930 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 71.640 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.226 12817 Z= 0.434 Angle : 0.890 17.899 17481 Z= 0.579 Chirality : 0.054 0.542 2002 Planarity : 0.005 0.069 2213 Dihedral : 15.990 85.231 4425 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.86 % Favored : 94.83 % Rotamer: Outliers : 3.75 % Allowed : 24.71 % Favored : 71.54 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1605 helix: -0.19 (1.11), residues: 23 sheet: 1.09 (0.21), residues: 617 loop : -1.56 (0.17), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 94 HIS 0.014 0.001 HIS F 89 PHE 0.027 0.001 PHE D 71 TYR 0.030 0.001 TYR B 221 ARG 0.011 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 78 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 62 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7137 (p90) outliers start: 51 outliers final: 15 residues processed: 127 average time/residue: 0.5544 time to fit residues: 103.0059 Evaluate side-chains 57 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12817 Z= 0.228 Angle : 0.516 4.603 17481 Z= 0.269 Chirality : 0.042 0.143 2002 Planarity : 0.004 0.043 2213 Dihedral : 5.449 56.267 1793 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.67 % Favored : 95.14 % Rotamer: Outliers : 1.99 % Allowed : 23.60 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1605 helix: -0.33 (1.09), residues: 24 sheet: 1.08 (0.21), residues: 621 loop : -1.47 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 465 HIS 0.003 0.001 HIS F 89 PHE 0.015 0.001 PHE D 71 TYR 0.009 0.001 TYR B 221 ARG 0.005 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 42 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7963 (t) REVERT: F 62 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7125 (p90) outliers start: 27 outliers final: 10 residues processed: 67 average time/residue: 0.3903 time to fit residues: 43.9495 Evaluate side-chains 50 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12817 Z= 0.284 Angle : 0.496 4.125 17481 Z= 0.260 Chirality : 0.042 0.139 2002 Planarity : 0.003 0.036 2213 Dihedral : 4.760 56.741 1775 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.55 % Favored : 94.21 % Rotamer: Outliers : 1.99 % Allowed : 22.72 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.69 (0.20), residues: 1605 helix: -0.06 (1.14), residues: 24 sheet: 0.89 (0.21), residues: 612 loop : -1.47 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 95 HIS 0.004 0.001 HIS A 144 PHE 0.010 0.001 PHE D 71 TYR 0.008 0.001 TYR A 221 ARG 0.003 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 32 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 MET cc_start: 0.7618 (mtt) cc_final: 0.7418 (mtt) REVERT: F 62 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7342 (p90) outliers start: 27 outliers final: 13 residues processed: 59 average time/residue: 0.4211 time to fit residues: 40.5364 Evaluate side-chains 45 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 31 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 93 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12817 Z= 0.274 Angle : 0.487 4.065 17481 Z= 0.254 Chirality : 0.042 0.139 2002 Planarity : 0.003 0.035 2213 Dihedral : 4.629 46.112 1774 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 1.76 % Allowed : 22.28 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.69 (0.20), residues: 1605 helix: 0.08 (1.15), residues: 24 sheet: 0.80 (0.21), residues: 606 loop : -1.39 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 406 HIS 0.004 0.001 HIS A 144 PHE 0.009 0.001 PHE D 71 TYR 0.009 0.001 TYR A 221 ARG 0.003 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 33 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 62 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7517 (p90) outliers start: 24 outliers final: 17 residues processed: 54 average time/residue: 0.4307 time to fit residues: 37.8153 Evaluate side-chains 49 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 31 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ASP Chi-restraints excluded: chain J residue 93 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12817 Z= 0.331 Angle : 0.501 4.408 17481 Z= 0.263 Chirality : 0.042 0.141 2002 Planarity : 0.003 0.035 2213 Dihedral : 4.532 44.632 1771 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.73 % Favored : 93.02 % Rotamer: Outliers : 1.99 % Allowed : 22.06 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.83 (0.20), residues: 1605 helix: -0.25 (1.09), residues: 24 sheet: 0.69 (0.20), residues: 610 loop : -1.48 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 406 HIS 0.005 0.001 HIS A 144 PHE 0.010 0.001 PHE D 71 TYR 0.008 0.001 TYR A 221 ARG 0.002 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 31 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7434 (ppt90) REVERT: F 62 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7616 (p90) outliers start: 27 outliers final: 19 residues processed: 58 average time/residue: 0.5298 time to fit residues: 46.6775 Evaluate side-chains 51 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 30 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 93 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12817 Z= 0.219 Angle : 0.464 4.015 17481 Z= 0.241 Chirality : 0.042 0.139 2002 Planarity : 0.003 0.037 2213 Dihedral : 4.406 43.719 1771 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.30 % Favored : 94.45 % Rotamer: Outliers : 1.54 % Allowed : 21.99 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.78 (0.20), residues: 1605 helix: 0.07 (1.01), residues: 30 sheet: 0.73 (0.20), residues: 608 loop : -1.46 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 406 HIS 0.003 0.001 HIS F 89 PHE 0.009 0.001 PHE D 71 TYR 0.008 0.001 TYR A 221 ARG 0.004 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 31 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 62 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7669 (p90) outliers start: 21 outliers final: 16 residues processed: 52 average time/residue: 0.4493 time to fit residues: 37.5647 Evaluate side-chains 47 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 30 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 93 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 158 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12817 Z= 0.329 Angle : 0.497 3.994 17481 Z= 0.260 Chirality : 0.041 0.148 2002 Planarity : 0.003 0.035 2213 Dihedral : 4.514 43.137 1771 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.73 % Favored : 93.02 % Rotamer: Outliers : 1.91 % Allowed : 21.54 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.94 (0.20), residues: 1605 helix: 0.01 (0.97), residues: 30 sheet: 0.59 (0.20), residues: 605 loop : -1.53 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 406 HIS 0.004 0.001 HIS A 144 PHE 0.009 0.001 PHE D 71 TYR 0.008 0.001 TYR A 221 ARG 0.003 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 30 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7387 (ppt90) REVERT: F 62 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7610 (p90) outliers start: 26 outliers final: 22 residues processed: 56 average time/residue: 0.4483 time to fit residues: 40.7968 Evaluate side-chains 54 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 30 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 93 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12817 Z= 0.216 Angle : 0.461 3.966 17481 Z= 0.239 Chirality : 0.042 0.139 2002 Planarity : 0.003 0.034 2213 Dihedral : 4.369 42.230 1771 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.30 % Favored : 94.45 % Rotamer: Outliers : 1.40 % Allowed : 21.84 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.84 (0.20), residues: 1605 helix: 0.43 (1.00), residues: 30 sheet: 0.65 (0.20), residues: 603 loop : -1.47 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 406 HIS 0.004 0.001 HIS F 89 PHE 0.008 0.001 PHE D 71 TYR 0.007 0.001 TYR A 221 ARG 0.003 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 30 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 62 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7663 (p90) outliers start: 19 outliers final: 18 residues processed: 49 average time/residue: 0.4868 time to fit residues: 37.5355 Evaluate side-chains 49 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 30 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 93 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12817 Z= 0.181 Angle : 0.446 3.988 17481 Z= 0.230 Chirality : 0.042 0.137 2002 Planarity : 0.003 0.034 2213 Dihedral : 4.208 40.537 1770 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.67 % Favored : 94.08 % Rotamer: Outliers : 1.32 % Allowed : 21.91 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.76 (0.20), residues: 1605 helix: 0.70 (1.01), residues: 30 sheet: 0.71 (0.21), residues: 602 loop : -1.42 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 406 HIS 0.004 0.000 HIS F 89 PHE 0.008 0.001 PHE D 71 TYR 0.007 0.001 TYR A 221 ARG 0.003 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 30 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 62 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7588 (p90) outliers start: 18 outliers final: 15 residues processed: 48 average time/residue: 0.4951 time to fit residues: 36.9946 Evaluate side-chains 46 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 30 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN B 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12817 Z= 0.307 Angle : 0.482 4.032 17481 Z= 0.251 Chirality : 0.041 0.136 2002 Planarity : 0.003 0.034 2213 Dihedral : 4.346 40.452 1770 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.54 % Favored : 93.27 % Rotamer: Outliers : 1.40 % Allowed : 21.62 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.91 (0.20), residues: 1605 helix: 0.37 (0.98), residues: 30 sheet: 0.60 (0.20), residues: 601 loop : -1.52 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 406 HIS 0.003 0.001 HIS A 144 PHE 0.008 0.001 PHE D 71 TYR 0.008 0.001 TYR A 221 ARG 0.002 0.000 ARG B 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 553 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 448 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 30 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 62 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7510 (p90) outliers start: 19 outliers final: 18 residues processed: 49 average time/residue: 0.4547 time to fit residues: 35.9281 Evaluate side-chains 49 residues out of total 1451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 30 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 133 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.042282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.034892 restraints weight = 216756.830| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 4.01 r_work: 0.2654 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12817 Z= 0.139 Angle : 0.440 4.196 17481 Z= 0.227 Chirality : 0.042 0.138 2002 Planarity : 0.003 0.034 2213 Dihedral : 4.149 39.236 1770 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.98 % Favored : 94.83 % Rotamer: Outliers : 1.25 % Allowed : 21.76 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.69 (0.20), residues: 1605 helix: 0.76 (1.00), residues: 30 sheet: 0.77 (0.21), residues: 602 loop : -1.39 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 406 HIS 0.004 0.000 HIS F 89 PHE 0.007 0.001 PHE D 71 TYR 0.007 0.001 TYR J 87 ARG 0.003 0.000 ARG B 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4038.55 seconds wall clock time: 71 minutes 37.57 seconds (4297.57 seconds total)