Starting phenix.real_space_refine on Thu Mar 21 09:49:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/03_2024/8u7v_42012_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/03_2024/8u7v_42012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/03_2024/8u7v_42012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/03_2024/8u7v_42012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/03_2024/8u7v_42012_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/03_2024/8u7v_42012_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 184 5.16 5 C 18456 2.51 5 N 5040 2.21 5 O 5904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 477": "OD1" <-> "OD2" Residue "D TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 477": "OD1" <-> "OD2" Residue "E TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 477": "OD1" <-> "OD2" Residue "F TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 477": "OD1" <-> "OD2" Residue "G TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 177": "OE1" <-> "OE2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 477": "OD1" <-> "OD2" Residue "H TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29680 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "B" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "C" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "D" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "F" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "G" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "H" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 15.15, per 1000 atoms: 0.51 Number of scatterers: 29680 At special positions: 0 Unit cell: (172.84, 172.84, 142.68, 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 184 16.00 P 96 15.00 O 5904 8.00 N 5040 7.00 C 18456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.47 Conformation dependent library (CDL) restraints added in 5.2 seconds 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 48 sheets defined 34.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.42 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 83 removed outlier: 3.725A pdb=" N ALA A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.929A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 356 removed outlier: 4.146A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 453 through 469 Proline residue: A 458 - end of helix removed outlier: 3.531A pdb=" N ILE A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 83 removed outlier: 3.724A pdb=" N ALA B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.927A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 343 through 356 removed outlier: 4.145A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 453 through 469 Proline residue: B 458 - end of helix removed outlier: 3.551A pdb=" N ILE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.719A pdb=" N ALA C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 127 through 136 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 255 through 266 Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.925A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 343 through 356 removed outlier: 4.150A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 453 through 469 Proline residue: C 458 - end of helix removed outlier: 3.534A pdb=" N ILE C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 83 removed outlier: 3.742A pdb=" N ALA D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 255 through 266 Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.926A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 356 removed outlier: 4.124A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 453 through 469 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 83 removed outlier: 3.742A pdb=" N ALA E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 255 through 266 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 3.926A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 356 removed outlier: 4.124A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 453 through 469 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 83 removed outlier: 3.725A pdb=" N ALA F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 127 through 136 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.928A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 343 through 356 removed outlier: 4.145A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 453 through 469 Proline residue: F 458 - end of helix removed outlier: 3.526A pdb=" N ILE F 464 " --> pdb=" O LEU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 83 removed outlier: 3.724A pdb=" N ALA G 81 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 127 through 136 Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 255 through 266 Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 3.927A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 343 through 356 removed outlier: 4.145A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 453 through 469 Proline residue: G 458 - end of helix removed outlier: 3.600A pdb=" N ILE G 464 " --> pdb=" O LEU G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 498 No H-bonds generated for 'chain 'G' and resid 495 through 498' Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.721A pdb=" N ALA H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 127 through 136 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 255 through 266 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 3.925A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 336 No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 343 through 356 removed outlier: 4.150A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 388 through 390 No H-bonds generated for 'chain 'H' and resid 388 through 390' Processing helix chain 'H' and resid 453 through 469 Proline residue: H 458 - end of helix removed outlier: 3.534A pdb=" N ILE H 464 " --> pdb=" O LEU H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 498 No H-bonds generated for 'chain 'H' and resid 495 through 498' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.568A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.453A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.600A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.525A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 208 through 212 removed outlier: 3.816A pdb=" N ILE A 222 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.560A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.446A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.595A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= L, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.826A pdb=" N ILE B 222 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.624A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.454A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.592A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 142 through 145 Processing sheet with id= R, first strand: chain 'C' and resid 208 through 212 removed outlier: 3.539A pdb=" N ILE C 222 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= T, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.571A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.453A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.597A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= X, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.811A pdb=" N ILE D 222 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.570A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.453A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.597A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 142 through 145 Processing sheet with id= AD, first strand: chain 'E' and resid 208 through 212 removed outlier: 3.811A pdb=" N ILE E 222 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.568A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.453A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.600A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.525A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 208 through 212 removed outlier: 3.816A pdb=" N ILE F 222 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AL, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.561A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.446A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AP, first strand: chain 'G' and resid 208 through 212 removed outlier: 3.826A pdb=" N ILE G 222 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AR, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.629A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.454A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.592A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'H' and resid 142 through 145 Processing sheet with id= AV, first strand: chain 'H' and resid 208 through 212 removed outlier: 3.539A pdb=" N ILE H 222 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2280 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: 9.77 Time building geometry restraints manager: 13.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4848 1.29 - 1.42: 7216 1.42 - 1.55: 17679 1.55 - 1.68: 161 1.68 - 1.81: 312 Bond restraints: 30216 Sorted by residual: bond pdb=" C5 IMP G 603 " pdb=" C6 IMP G 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C5 IMP C 603 " pdb=" C6 IMP C 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C5 IMP D 603 " pdb=" C6 IMP D 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C5 IMP H 603 " pdb=" C6 IMP H 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C5 IMP B 603 " pdb=" C6 IMP B 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 ... (remaining 30211 not shown) Histogram of bond angle deviations from ideal: 94.48 - 104.11: 659 104.11 - 113.74: 17908 113.74 - 123.37: 21562 123.37 - 133.00: 967 133.00 - 142.63: 24 Bond angle restraints: 41120 Sorted by residual: angle pdb=" PA ATP A 604 " pdb=" O3A ATP A 604 " pdb=" PB ATP A 604 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PA ATP F 604 " pdb=" O3A ATP F 604 " pdb=" PB ATP F 604 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PA ATP D 604 " pdb=" O3A ATP D 604 " pdb=" PB ATP D 604 " ideal model delta sigma weight residual 136.83 124.03 12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" PA ATP E 604 " pdb=" O3A ATP E 604 " pdb=" PB ATP E 604 " ideal model delta sigma weight residual 136.83 124.05 12.78 1.00e+00 1.00e+00 1.63e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 124.09 12.74 1.00e+00 1.00e+00 1.62e+02 ... (remaining 41115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 17612 35.18 - 70.37: 631 70.37 - 105.55: 87 105.55 - 140.74: 14 140.74 - 175.92: 48 Dihedral angle restraints: 18392 sinusoidal: 7768 harmonic: 10624 Sorted by residual: dihedral pdb=" O5' GTP B 601 " pdb=" O3A GTP B 601 " pdb=" PA GTP B 601 " pdb=" PB GTP B 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.20 175.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP G 601 " pdb=" O3A GTP G 601 " pdb=" PA GTP G 601 " pdb=" PB GTP G 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.27 175.85 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP D 601 " pdb=" O3A GTP D 601 " pdb=" PA GTP D 601 " pdb=" PB GTP D 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.51 175.61 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 18389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 4664 0.203 - 0.405: 88 0.405 - 0.608: 8 0.608 - 0.810: 0 0.810 - 1.013: 16 Chirality restraints: 4776 Sorted by residual: chirality pdb=" C4' IMP F 603 " pdb=" C3' IMP F 603 " pdb=" C5' IMP F 603 " pdb=" O4' IMP F 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" C4' IMP A 603 " pdb=" C3' IMP A 603 " pdb=" C5' IMP A 603 " pdb=" O4' IMP A 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" C4' IMP E 603 " pdb=" C3' IMP E 603 " pdb=" C5' IMP E 603 " pdb=" O4' IMP E 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 4773 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 180 " 0.079 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO H 181 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO H 181 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 181 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR E 180 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C THR E 180 " 0.052 2.00e-02 2.50e+03 pdb=" O THR E 180 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO E 181 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 180 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C THR G 180 " -0.051 2.00e-02 2.50e+03 pdb=" O THR G 180 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO G 181 " 0.017 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 783 2.68 - 3.24: 30299 3.24 - 3.79: 44626 3.79 - 4.35: 63138 4.35 - 4.90: 105097 Nonbonded interactions: 243943 Sorted by model distance: nonbonded pdb=" O VAL E 73 " pdb=" OG1 THR E 74 " model vdw 2.127 2.440 nonbonded pdb=" O VAL H 73 " pdb=" OG1 THR H 74 " model vdw 2.128 2.440 nonbonded pdb=" O VAL C 73 " pdb=" OG1 THR C 74 " model vdw 2.128 2.440 nonbonded pdb=" O VAL D 73 " pdb=" OG1 THR D 74 " model vdw 2.130 2.440 nonbonded pdb=" O VAL G 73 " pdb=" OG1 THR G 74 " model vdw 2.133 2.440 ... (remaining 243938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.500 Check model and map are aligned: 0.440 Set scattering table: 0.290 Process input model: 78.550 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.230 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.007 0.157 30216 Z= 0.435 Angle : 1.179 22.127 41120 Z= 0.607 Chirality : 0.089 1.013 4776 Planarity : 0.005 0.108 5056 Dihedral : 20.780 175.921 11608 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.27 % Favored : 96.52 % Rotamer: Outliers : 0.85 % Allowed : 11.98 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 3704 helix: -0.08 (0.14), residues: 1376 sheet: -0.61 (0.32), residues: 216 loop : -0.98 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 507 PHE 0.013 0.001 PHE B 456 TYR 0.013 0.001 TYR D 509 ARG 0.003 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 349 time to evaluate : 3.303 Fit side-chains REVERT: A 327 CYS cc_start: 0.8339 (p) cc_final: 0.7988 (p) REVERT: B 327 CYS cc_start: 0.8319 (p) cc_final: 0.7987 (p) REVERT: C 327 CYS cc_start: 0.8288 (p) cc_final: 0.7961 (p) REVERT: D 327 CYS cc_start: 0.8307 (p) cc_final: 0.7969 (p) REVERT: E 327 CYS cc_start: 0.8300 (p) cc_final: 0.7970 (p) REVERT: F 327 CYS cc_start: 0.8341 (p) cc_final: 0.7993 (p) REVERT: G 327 CYS cc_start: 0.8317 (p) cc_final: 0.7988 (p) REVERT: H 327 CYS cc_start: 0.8255 (p) cc_final: 0.7954 (p) outliers start: 26 outliers final: 11 residues processed: 373 average time/residue: 0.3403 time to fit residues: 215.5973 Evaluate side-chains 317 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 306 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.9980 chunk 284 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN D 33 ASN E 33 ASN F 33 ASN G 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30216 Z= 0.276 Angle : 0.671 7.662 41120 Z= 0.329 Chirality : 0.047 0.165 4776 Planarity : 0.005 0.055 5056 Dihedral : 19.960 156.738 5014 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.43 % Favored : 96.36 % Rotamer: Outliers : 1.76 % Allowed : 11.98 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3704 helix: -0.01 (0.14), residues: 1368 sheet: -0.18 (0.29), residues: 280 loop : -0.69 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 93 PHE 0.010 0.002 PHE A 35 TYR 0.008 0.001 TYR F 282 ARG 0.004 0.000 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 323 time to evaluate : 3.587 Fit side-chains REVERT: A 144 ILE cc_start: 0.7815 (mm) cc_final: 0.7406 (mm) REVERT: B 144 ILE cc_start: 0.8071 (mm) cc_final: 0.7764 (mm) REVERT: D 144 ILE cc_start: 0.8050 (mm) cc_final: 0.7740 (mm) REVERT: E 144 ILE cc_start: 0.8046 (mm) cc_final: 0.7744 (mm) REVERT: F 144 ILE cc_start: 0.7807 (mm) cc_final: 0.7403 (mm) REVERT: G 144 ILE cc_start: 0.8035 (mm) cc_final: 0.7713 (mm) outliers start: 54 outliers final: 38 residues processed: 366 average time/residue: 0.3272 time to fit residues: 210.9958 Evaluate side-chains 331 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 293 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 342 optimal weight: 0.8980 chunk 369 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 339 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 274 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN B 198 ASN C 198 ASN D 198 ASN E 198 ASN F 198 ASN F 469 GLN G 198 ASN H 198 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30216 Z= 0.248 Angle : 0.611 7.095 41120 Z= 0.300 Chirality : 0.045 0.170 4776 Planarity : 0.004 0.052 5056 Dihedral : 18.531 159.161 5008 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.13 % Favored : 96.65 % Rotamer: Outliers : 2.60 % Allowed : 13.31 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3704 helix: 0.12 (0.14), residues: 1336 sheet: 0.06 (0.30), residues: 280 loop : -0.61 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 125 PHE 0.015 0.002 PHE G 139 TYR 0.009 0.001 TYR A 348 ARG 0.003 0.000 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 339 time to evaluate : 3.171 Fit side-chains REVERT: A 144 ILE cc_start: 0.8216 (mm) cc_final: 0.7868 (mt) REVERT: C 135 MET cc_start: 0.7937 (tmm) cc_final: 0.7511 (tmm) REVERT: C 144 ILE cc_start: 0.8197 (mm) cc_final: 0.7975 (mm) REVERT: D 135 MET cc_start: 0.7961 (tmm) cc_final: 0.7542 (tmm) REVERT: E 135 MET cc_start: 0.7957 (tmm) cc_final: 0.7535 (tmm) REVERT: F 144 ILE cc_start: 0.8209 (mm) cc_final: 0.7862 (mt) REVERT: F 469 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: H 135 MET cc_start: 0.7966 (tmm) cc_final: 0.7544 (tmm) REVERT: H 144 ILE cc_start: 0.8269 (mm) cc_final: 0.8021 (mm) outliers start: 80 outliers final: 52 residues processed: 396 average time/residue: 0.3351 time to fit residues: 227.7441 Evaluate side-chains 373 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 320 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 163 optimal weight: 0.0470 chunk 229 optimal weight: 0.7980 chunk 343 optimal weight: 1.9990 chunk 363 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30216 Z= 0.191 Angle : 0.579 8.107 41120 Z= 0.278 Chirality : 0.044 0.178 4776 Planarity : 0.004 0.049 5056 Dihedral : 17.743 157.549 5000 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.43 % Favored : 96.36 % Rotamer: Outliers : 2.31 % Allowed : 14.78 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3704 helix: 0.24 (0.14), residues: 1360 sheet: 0.10 (0.29), residues: 280 loop : -0.38 (0.15), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 137 PHE 0.010 0.001 PHE A 456 TYR 0.008 0.001 TYR C 348 ARG 0.002 0.000 ARG H 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 360 time to evaluate : 3.390 Fit side-chains REVERT: A 135 MET cc_start: 0.7999 (ttm) cc_final: 0.7714 (tmm) REVERT: A 144 ILE cc_start: 0.8436 (mm) cc_final: 0.8056 (mt) REVERT: A 260 LEU cc_start: 0.8724 (tt) cc_final: 0.8497 (tp) REVERT: A 448 GLN cc_start: 0.6953 (mt0) cc_final: 0.6728 (tt0) REVERT: B 135 MET cc_start: 0.8063 (ttm) cc_final: 0.7732 (tmm) REVERT: B 483 MET cc_start: 0.8930 (tmm) cc_final: 0.8713 (tmm) REVERT: C 135 MET cc_start: 0.7933 (tmm) cc_final: 0.7493 (tmm) REVERT: C 260 LEU cc_start: 0.8725 (tt) cc_final: 0.8524 (tp) REVERT: C 483 MET cc_start: 0.8858 (tmm) cc_final: 0.8644 (tmm) REVERT: D 135 MET cc_start: 0.7955 (tmm) cc_final: 0.7496 (tmm) REVERT: D 483 MET cc_start: 0.8836 (tmm) cc_final: 0.8626 (tmm) REVERT: E 135 MET cc_start: 0.7953 (tmm) cc_final: 0.7489 (tmm) REVERT: F 135 MET cc_start: 0.8001 (ttm) cc_final: 0.7717 (tmm) REVERT: F 144 ILE cc_start: 0.8435 (mm) cc_final: 0.8061 (mt) REVERT: F 260 LEU cc_start: 0.8723 (tt) cc_final: 0.8498 (tp) REVERT: F 448 GLN cc_start: 0.6811 (mt0) cc_final: 0.6609 (tt0) REVERT: F 483 MET cc_start: 0.8945 (tmm) cc_final: 0.8743 (tmm) REVERT: G 135 MET cc_start: 0.8038 (ttm) cc_final: 0.7731 (tmm) REVERT: G 483 MET cc_start: 0.8947 (tmm) cc_final: 0.8715 (tmm) REVERT: H 135 MET cc_start: 0.7975 (tmm) cc_final: 0.7418 (tmm) REVERT: H 483 MET cc_start: 0.8838 (tmm) cc_final: 0.8613 (tmm) outliers start: 71 outliers final: 48 residues processed: 410 average time/residue: 0.3747 time to fit residues: 253.9167 Evaluate side-chains 344 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 296 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 270 optimal weight: 0.0770 chunk 149 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 0.0070 chunk 0 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 441 GLN E 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30216 Z= 0.185 Angle : 0.566 6.789 41120 Z= 0.271 Chirality : 0.044 0.163 4776 Planarity : 0.004 0.044 5056 Dihedral : 17.448 158.604 5000 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.29 % Favored : 96.49 % Rotamer: Outliers : 3.39 % Allowed : 14.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3704 helix: 0.35 (0.14), residues: 1352 sheet: 0.11 (0.29), residues: 280 loop : -0.25 (0.15), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 137 PHE 0.010 0.001 PHE E 35 TYR 0.008 0.001 TYR A 348 ARG 0.001 0.000 ARG F 412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 310 time to evaluate : 3.367 Fit side-chains REVERT: A 144 ILE cc_start: 0.8397 (mm) cc_final: 0.8183 (mt) REVERT: A 260 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8404 (tp) REVERT: B 483 MET cc_start: 0.9074 (tmm) cc_final: 0.8840 (tmm) REVERT: C 135 MET cc_start: 0.7855 (tmm) cc_final: 0.7358 (tmm) REVERT: C 260 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8406 (tp) REVERT: C 483 MET cc_start: 0.8955 (tmm) cc_final: 0.8724 (tmm) REVERT: D 500 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5275 (mt-10) REVERT: E 500 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5271 (mt-10) REVERT: F 144 ILE cc_start: 0.8393 (mm) cc_final: 0.8183 (mt) REVERT: F 260 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8408 (tp) REVERT: F 483 MET cc_start: 0.9037 (tmm) cc_final: 0.8814 (tmm) REVERT: G 483 MET cc_start: 0.9083 (tmm) cc_final: 0.8840 (tmm) REVERT: H 483 MET cc_start: 0.8938 (tmm) cc_final: 0.8691 (tmm) outliers start: 104 outliers final: 60 residues processed: 370 average time/residue: 0.3480 time to fit residues: 218.9897 Evaluate side-chains 363 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 298 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30216 Z= 0.418 Angle : 0.687 7.812 41120 Z= 0.338 Chirality : 0.049 0.180 4776 Planarity : 0.004 0.042 5056 Dihedral : 18.093 160.190 5000 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.51 % Favored : 94.28 % Rotamer: Outliers : 3.22 % Allowed : 15.07 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3704 helix: -0.09 (0.14), residues: 1336 sheet: -0.09 (0.29), residues: 280 loop : -0.71 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 372 PHE 0.015 0.002 PHE D 35 TYR 0.011 0.002 TYR A 348 ARG 0.003 0.000 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 292 time to evaluate : 3.253 Fit side-chains REVERT: D 483 MET cc_start: 0.8878 (tmm) cc_final: 0.8559 (tmm) outliers start: 99 outliers final: 69 residues processed: 378 average time/residue: 0.3448 time to fit residues: 223.1325 Evaluate side-chains 335 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 266 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 0.6980 chunk 203 optimal weight: 7.9990 chunk 362 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN B 33 ASN B 441 GLN G 33 ASN H 441 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30216 Z= 0.196 Angle : 0.575 8.262 41120 Z= 0.278 Chirality : 0.044 0.166 4776 Planarity : 0.004 0.038 5056 Dihedral : 17.474 161.562 5000 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.83 % Favored : 96.95 % Rotamer: Outliers : 3.39 % Allowed : 16.02 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3704 helix: 0.30 (0.15), residues: 1328 sheet: -0.11 (0.29), residues: 280 loop : -0.52 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 507 PHE 0.010 0.001 PHE A 456 TYR 0.009 0.001 TYR C 348 ARG 0.001 0.000 ARG D 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 284 time to evaluate : 3.350 Fit side-chains REVERT: A 500 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5344 (mt-10) REVERT: D 483 MET cc_start: 0.9066 (tmm) cc_final: 0.8840 (tmm) REVERT: F 483 MET cc_start: 0.9017 (tmm) cc_final: 0.8816 (tmm) REVERT: F 500 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5333 (mt-10) REVERT: G 483 MET cc_start: 0.9057 (tmm) cc_final: 0.8833 (tmm) outliers start: 104 outliers final: 67 residues processed: 363 average time/residue: 0.3540 time to fit residues: 217.8700 Evaluate side-chains 331 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 262 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN F 33 ASN F 441 GLN G 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 30216 Z= 0.256 Angle : 0.598 7.978 41120 Z= 0.291 Chirality : 0.045 0.165 4776 Planarity : 0.004 0.035 5056 Dihedral : 17.462 162.608 5000 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.37 % Favored : 95.44 % Rotamer: Outliers : 3.22 % Allowed : 16.80 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3704 helix: 0.12 (0.14), residues: 1344 sheet: -0.43 (0.27), residues: 360 loop : -0.60 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 372 PHE 0.013 0.002 PHE A 35 TYR 0.009 0.001 TYR A 348 ARG 0.002 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 272 time to evaluate : 3.596 Fit side-chains REVERT: F 483 MET cc_start: 0.8937 (tmm) cc_final: 0.8671 (tmm) REVERT: G 483 MET cc_start: 0.8937 (tmm) cc_final: 0.8718 (tmm) outliers start: 99 outliers final: 86 residues processed: 357 average time/residue: 0.3512 time to fit residues: 212.6578 Evaluate side-chains 337 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 251 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 chunk 316 optimal weight: 0.8980 chunk 337 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 319 optimal weight: 0.5980 chunk 336 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN D 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30216 Z= 0.210 Angle : 0.571 7.586 41120 Z= 0.277 Chirality : 0.044 0.168 4776 Planarity : 0.004 0.036 5056 Dihedral : 17.249 164.092 5000 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.59 % Favored : 96.19 % Rotamer: Outliers : 2.96 % Allowed : 17.32 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3704 helix: 0.25 (0.14), residues: 1344 sheet: -0.41 (0.27), residues: 360 loop : -0.55 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 507 PHE 0.011 0.001 PHE D 35 TYR 0.014 0.001 TYR E 509 ARG 0.001 0.000 ARG H 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 273 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 483 MET cc_start: 0.9022 (tmm) cc_final: 0.8819 (tmm) REVERT: F 483 MET cc_start: 0.9028 (tmm) cc_final: 0.8781 (tmm) REVERT: G 483 MET cc_start: 0.9054 (tmm) cc_final: 0.8832 (tmm) outliers start: 91 outliers final: 79 residues processed: 353 average time/residue: 0.3535 time to fit residues: 212.1428 Evaluate side-chains 334 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 255 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 374 optimal weight: 7.9990 chunk 344 optimal weight: 6.9990 chunk 298 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 441 GLN D 441 GLN E 33 ASN E 441 GLN F 441 GLN F 448 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30216 Z= 0.274 Angle : 0.597 7.413 41120 Z= 0.293 Chirality : 0.045 0.165 4776 Planarity : 0.004 0.041 5056 Dihedral : 17.327 164.913 5000 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.40 % Favored : 95.41 % Rotamer: Outliers : 3.09 % Allowed : 17.12 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3704 helix: 0.08 (0.14), residues: 1344 sheet: -0.45 (0.27), residues: 360 loop : -0.64 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 507 PHE 0.013 0.002 PHE E 35 TYR 0.013 0.001 TYR A 509 ARG 0.002 0.000 ARG B 480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 259 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 483 MET cc_start: 0.8847 (tmm) cc_final: 0.8644 (tmm) REVERT: D 483 MET cc_start: 0.8931 (tmm) cc_final: 0.8681 (tmm) REVERT: F 483 MET cc_start: 0.8944 (tmm) cc_final: 0.8665 (tmm) REVERT: G 483 MET cc_start: 0.8950 (tmm) cc_final: 0.8708 (tmm) outliers start: 95 outliers final: 81 residues processed: 342 average time/residue: 0.3464 time to fit residues: 200.8440 Evaluate side-chains 339 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 258 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 275 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 0.0770 chunk 298 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 441 GLN E 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.131034 restraints weight = 38180.587| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.52 r_work: 0.3614 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30216 Z= 0.221 Angle : 0.572 7.246 41120 Z= 0.280 Chirality : 0.044 0.172 4776 Planarity : 0.004 0.040 5056 Dihedral : 17.171 165.762 5000 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.48 % Favored : 96.30 % Rotamer: Outliers : 2.80 % Allowed : 17.61 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3704 helix: 0.41 (0.15), residues: 1296 sheet: -0.43 (0.27), residues: 360 loop : -0.57 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 507 PHE 0.010 0.001 PHE A 456 TYR 0.014 0.001 TYR F 509 ARG 0.002 0.000 ARG C 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6095.87 seconds wall clock time: 111 minutes 8.50 seconds (6668.50 seconds total)