Starting phenix.real_space_refine on Tue Mar 19 06:16:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/03_2024/3jd0_6631_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/03_2024/3jd0_6631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/03_2024/3jd0_6631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/03_2024/3jd0_6631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/03_2024/3jd0_6631_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/03_2024/3jd0_6631_updated.pdb" } resolution = 3.47 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= 0.001 sd= 0.004 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 18 5.49 5 S 114 5.16 5 C 14784 2.51 5 N 4104 2.21 5 O 4458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23478 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "B" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "C" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "D" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "E" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "F" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.57, per 1000 atoms: 0.49 Number of scatterers: 23478 At special positions: 0 Unit cell: (111.569, 123.045, 161.298, 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 114 16.00 P 18 15.00 O 4458 8.00 N 4104 7.00 C 14784 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: 9.21 Conformation dependent library (CDL) restraints added in 4.0 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 18 sheets defined 49.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.977A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 51 removed outlier: 3.768A pdb=" N SER A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.589A pdb=" N ALA A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.757A pdb=" N ARG A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.659A pdb=" N HIS A 195 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 211 through 227 removed outlier: 4.318A pdb=" N THR A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.915A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 297 removed outlier: 3.519A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' 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 354 through 363 Processing helix chain 'A' and resid 370 through 387 removed outlier: 4.465A pdb=" N GLY A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 420 removed outlier: 4.719A pdb=" N LEU A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 441 Processing helix chain 'A' and resid 445 through 471 removed outlier: 3.808A pdb=" N THR A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 496 Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.977A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 51 removed outlier: 3.767A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.589A pdb=" N ALA B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 138 through 154 removed outlier: 3.758A pdb=" N ARG B 146 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 185 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.659A pdb=" N HIS B 195 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 211 through 227 removed outlier: 4.317A pdb=" N THR B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 233 No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.915A pdb=" N PHE B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 removed outlier: 3.519A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' 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 354 through 363 Processing helix chain 'B' and resid 370 through 387 removed outlier: 4.464A pdb=" N GLY B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 420 removed outlier: 4.720A pdb=" N LEU B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 445 through 471 removed outlier: 3.808A pdb=" N THR B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 496 Processing helix chain 'C' and resid 9 through 28 removed outlier: 3.977A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 51 removed outlier: 3.768A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 118 removed outlier: 3.589A pdb=" N ALA C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 138 through 154 removed outlier: 3.758A pdb=" N ARG C 146 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.659A pdb=" N HIS C 195 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 211 through 227 removed outlier: 4.317A pdb=" N THR C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 233 No H-bonds generated for 'chain 'C' and resid 230 through 233' Processing helix chain 'C' and resid 256 through 266 removed outlier: 3.915A pdb=" N PHE C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 297 removed outlier: 3.519A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' 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 354 through 363 Processing helix chain 'C' and resid 370 through 387 removed outlier: 4.465A pdb=" N GLY C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C 378 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 420 removed outlier: 4.720A pdb=" N LEU C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 441 Processing helix chain 'C' and resid 445 through 471 removed outlier: 3.808A pdb=" N THR C 456 " --> pdb=" O GLY C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 496 Processing helix chain 'D' and resid 9 through 28 removed outlier: 3.977A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 51 removed outlier: 3.767A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 118 removed outlier: 3.589A pdb=" N ALA D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 135 No H-bonds generated for 'chain 'D' and resid 133 through 135' Processing helix chain 'D' and resid 138 through 154 removed outlier: 3.757A pdb=" N ARG D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 185 Processing helix chain 'D' and resid 192 through 196 removed outlier: 3.658A pdb=" N HIS D 195 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 211 through 227 removed outlier: 4.318A pdb=" N THR D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 233 No H-bonds generated for 'chain 'D' and resid 230 through 233' Processing helix chain 'D' and resid 256 through 266 removed outlier: 3.914A pdb=" N PHE D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.519A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' 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 354 through 363 Processing helix chain 'D' and resid 370 through 387 removed outlier: 4.465A pdb=" N GLY D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLY D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL D 378 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 420 removed outlier: 4.719A pdb=" N LEU D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 441 Processing helix chain 'D' and resid 445 through 471 removed outlier: 3.808A pdb=" N THR D 456 " --> pdb=" O GLY D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 496 Processing helix chain 'E' and resid 9 through 28 removed outlier: 3.977A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 51 removed outlier: 3.768A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 118 removed outlier: 3.589A pdb=" N ALA E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 138 through 154 removed outlier: 3.758A pdb=" N ARG E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 153 " --> pdb=" O THR E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 185 Processing helix chain 'E' and resid 192 through 196 removed outlier: 3.659A pdb=" N HIS E 195 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 211 through 227 removed outlier: 4.318A pdb=" N THR E 215 " --> pdb=" O ARG E 211 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY E 216 " --> pdb=" O ILE E 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 233 No H-bonds generated for 'chain 'E' and resid 230 through 233' Processing helix chain 'E' and resid 256 through 266 removed outlier: 3.914A pdb=" N PHE E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 297 removed outlier: 3.519A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 316 No H-bonds generated for 'chain 'E' and resid 314 through 316' 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 354 through 363 Processing helix chain 'E' and resid 370 through 387 removed outlier: 4.464A pdb=" N GLY E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLY E 377 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL E 378 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 420 removed outlier: 4.720A pdb=" N LEU E 410 " --> pdb=" O ASN E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 441 Processing helix chain 'E' and resid 445 through 471 removed outlier: 3.809A pdb=" N THR E 456 " --> pdb=" O GLY E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 496 Processing helix chain 'F' and resid 9 through 28 removed outlier: 3.977A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 51 removed outlier: 3.768A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 118 removed outlier: 3.589A pdb=" N ALA F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 138 through 154 removed outlier: 3.758A pdb=" N ARG F 146 " --> pdb=" O GLU F 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 185 Processing helix chain 'F' and resid 192 through 196 removed outlier: 3.659A pdb=" N HIS F 195 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 211 through 227 removed outlier: 4.318A pdb=" N THR F 215 " --> pdb=" O ARG F 211 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY F 216 " --> pdb=" O ILE F 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 233 No H-bonds generated for 'chain 'F' and resid 230 through 233' Processing helix chain 'F' and resid 256 through 266 removed outlier: 3.914A pdb=" N PHE F 266 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 297 removed outlier: 3.519A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' 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 354 through 363 Processing helix chain 'F' and resid 370 through 387 removed outlier: 4.464A pdb=" N GLY F 376 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLY F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL F 378 " --> pdb=" O ASN F 374 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER F 381 " --> pdb=" O GLY F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 420 removed outlier: 4.720A pdb=" N LEU F 410 " --> pdb=" O ASN F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 441 Processing helix chain 'F' and resid 445 through 471 removed outlier: 3.809A pdb=" N THR F 456 " --> pdb=" O GLY F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 496 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= B, first strand: chain 'A' and resid 63 through 66 Processing sheet with id= C, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.831A pdb=" N VAL A 273 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= E, first strand: chain 'B' and resid 63 through 66 Processing sheet with id= F, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.832A pdb=" N VAL B 273 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= H, first strand: chain 'C' and resid 63 through 66 Processing sheet with id= I, first strand: chain 'C' and resid 272 through 275 removed outlier: 3.831A pdb=" N VAL C 273 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= K, first strand: chain 'D' and resid 63 through 66 Processing sheet with id= L, first strand: chain 'D' and resid 272 through 275 removed outlier: 3.832A pdb=" N VAL D 273 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= N, first strand: chain 'E' and resid 63 through 66 Processing sheet with id= O, first strand: chain 'E' and resid 272 through 275 removed outlier: 3.832A pdb=" N VAL E 273 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 57 through 60 Processing sheet with id= Q, first strand: chain 'F' and resid 63 through 66 Processing sheet with id= R, first strand: chain 'F' and resid 272 through 275 removed outlier: 3.832A pdb=" N VAL F 273 " --> pdb=" O ILE F 280 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 10.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7782 1.34 - 1.46: 5523 1.46 - 1.58: 10461 1.58 - 1.69: 30 1.69 - 1.81: 192 Bond restraints: 23988 Sorted by residual: bond pdb=" CB VAL D 449 " pdb=" CG1 VAL D 449 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB VAL E 449 " pdb=" CG1 VAL E 449 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.50e+00 bond pdb=" CB VAL A 449 " pdb=" CG1 VAL A 449 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" CB VAL B 449 " pdb=" CG1 VAL B 449 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.40e+00 bond pdb=" CB VAL C 449 " pdb=" CG1 VAL C 449 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.35e+00 ... (remaining 23983 not shown) Histogram of bond angle deviations from ideal: 96.97 - 104.39: 410 104.39 - 111.81: 11726 111.81 - 119.23: 7615 119.23 - 126.66: 12414 126.66 - 134.08: 277 Bond angle restraints: 32442 Sorted by residual: angle pdb=" CA LEU B 371 " pdb=" CB LEU B 371 " pdb=" CG LEU B 371 " ideal model delta sigma weight residual 116.30 125.66 -9.36 3.50e+00 8.16e-02 7.16e+00 angle pdb=" CA LEU C 371 " pdb=" CB LEU C 371 " pdb=" CG LEU C 371 " ideal model delta sigma weight residual 116.30 125.65 -9.35 3.50e+00 8.16e-02 7.14e+00 angle pdb=" CA LEU E 371 " pdb=" CB LEU E 371 " pdb=" CG LEU E 371 " ideal model delta sigma weight residual 116.30 125.64 -9.34 3.50e+00 8.16e-02 7.13e+00 angle pdb=" CA LEU A 371 " pdb=" CB LEU A 371 " pdb=" CG LEU A 371 " ideal model delta sigma weight residual 116.30 125.64 -9.34 3.50e+00 8.16e-02 7.12e+00 angle pdb=" CA LEU D 371 " pdb=" CB LEU D 371 " pdb=" CG LEU D 371 " ideal model delta sigma weight residual 116.30 125.64 -9.34 3.50e+00 8.16e-02 7.12e+00 ... (remaining 32437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 14268 35.85 - 71.71: 42 71.71 - 107.56: 6 107.56 - 143.41: 6 143.41 - 179.27: 12 Dihedral angle restraints: 14334 sinusoidal: 5856 harmonic: 8478 Sorted by residual: dihedral pdb=" C5' GTP F 601 " pdb=" O5' GTP F 601 " pdb=" PA GTP F 601 " pdb=" O3A GTP F 601 " ideal model delta sinusoidal sigma weight residual 69.27 -110.00 179.27 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP D 601 " pdb=" O5' GTP D 601 " pdb=" PA GTP D 601 " pdb=" O3A GTP D 601 " ideal model delta sinusoidal sigma weight residual 69.27 -109.99 179.26 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP E 601 " pdb=" O5' GTP E 601 " pdb=" PA GTP E 601 " pdb=" O3A GTP E 601 " ideal model delta sinusoidal sigma weight residual 69.27 -109.98 179.25 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 14331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1725 0.029 - 0.058: 943 0.058 - 0.087: 516 0.087 - 0.116: 213 0.116 - 0.145: 119 Chirality restraints: 3516 Sorted by residual: chirality pdb=" CB THR F 456 " pdb=" CA THR F 456 " pdb=" OG1 THR F 456 " pdb=" CG2 THR F 456 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA TYR E 407 " pdb=" N TYR E 407 " pdb=" C TYR E 407 " pdb=" CB TYR E 407 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CB THR A 456 " pdb=" CA THR A 456 " pdb=" OG1 THR A 456 " pdb=" CG2 THR A 456 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 3513 not shown) Planarity restraints: 4194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 166 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO E 167 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 167 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 167 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 166 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO F 167 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 166 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO C 167 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 167 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 167 " 0.030 5.00e-02 4.00e+02 ... (remaining 4191 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 447 2.57 - 3.15: 24078 3.15 - 3.74: 35197 3.74 - 4.32: 54803 4.32 - 4.90: 85372 Nonbonded interactions: 199897 Sorted by model distance: nonbonded pdb=" O LEU B 409 " pdb=" OG SER B 412 " model vdw 1.989 2.440 nonbonded pdb=" O LEU E 409 " pdb=" OG SER E 412 " model vdw 1.989 2.440 nonbonded pdb=" O LEU A 409 " pdb=" OG SER A 412 " model vdw 1.989 2.440 nonbonded pdb=" O LEU C 409 " pdb=" OG SER C 412 " model vdw 1.989 2.440 nonbonded pdb=" O LEU F 409 " pdb=" OG SER F 412 " model vdw 1.989 2.440 ... (remaining 199892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 5.140 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 60.190 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.190 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:3.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.072 23988 Z= 0.780 Angle : 0.817 9.363 32442 Z= 0.478 Chirality : 0.050 0.145 3516 Planarity : 0.005 0.055 4194 Dihedral : 10.314 179.267 8934 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.81 % Allowed : 13.26 % Favored : 85.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -5.89 (0.10), residues: 2964 helix: -4.31 (0.07), residues: 1488 sheet: -2.62 (0.24), residues: 330 loop : -3.45 (0.14), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 281 HIS 0.007 0.002 HIS A 57 PHE 0.020 0.002 PHE F 421 TYR 0.013 0.002 TYR F 382 ARG 0.007 0.001 ARG F 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8193 (mp) cc_final: 0.7822 (mm) REVERT: A 364 ASN cc_start: 0.8465 (t0) cc_final: 0.8259 (t0) REVERT: B 187 ILE cc_start: 0.8347 (mm) cc_final: 0.8146 (mm) REVERT: B 384 GLU cc_start: 0.8034 (tt0) cc_final: 0.7749 (tt0) REVERT: C 315 LEU cc_start: 0.8203 (mp) cc_final: 0.7992 (mm) REVERT: D 315 LEU cc_start: 0.8188 (mp) cc_final: 0.7830 (mm) REVERT: D 364 ASN cc_start: 0.8463 (t0) cc_final: 0.8258 (t0) REVERT: E 384 GLU cc_start: 0.8036 (tt0) cc_final: 0.7752 (tt0) REVERT: F 315 LEU cc_start: 0.8203 (mp) cc_final: 0.7995 (mm) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.4091 time to fit residues: 322.4762 Evaluate side-chains 264 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 HIS ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23988 Z= 0.306 Angle : 0.709 10.642 32442 Z= 0.360 Chirality : 0.045 0.173 3516 Planarity : 0.005 0.041 4194 Dihedral : 13.102 169.519 3342 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.80 % Favored : 93.99 % Rotamer: Outliers : 1.32 % Allowed : 5.97 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.48 (0.14), residues: 2964 helix: -1.12 (0.12), residues: 1506 sheet: -1.93 (0.24), residues: 330 loop : -2.10 (0.16), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 72 HIS 0.013 0.001 HIS D 189 PHE 0.029 0.003 PHE E 16 TYR 0.027 0.002 TYR D 407 ARG 0.003 0.000 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 328 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 MET cc_start: 0.8040 (mmp) cc_final: 0.7821 (mmt) REVERT: B 384 GLU cc_start: 0.7813 (tt0) cc_final: 0.7573 (tt0) REVERT: B 402 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7486 (mt-10) REVERT: C 181 ASP cc_start: 0.7695 (t0) cc_final: 0.7428 (t0) REVERT: E 169 MET cc_start: 0.8050 (mmp) cc_final: 0.7827 (mmt) REVERT: E 384 GLU cc_start: 0.7809 (tt0) cc_final: 0.7581 (tt0) REVERT: E 402 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7483 (mt-10) REVERT: F 181 ASP cc_start: 0.7694 (t0) cc_final: 0.7431 (t0) outliers start: 33 outliers final: 21 residues processed: 351 average time/residue: 0.3103 time to fit residues: 177.4558 Evaluate side-chains 257 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 236 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 411 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 222 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 chunk 267 optimal weight: 2.9990 chunk 288 optimal weight: 9.9990 chunk 238 optimal weight: 30.0000 chunk 265 optimal weight: 8.9990 chunk 91 optimal weight: 30.0000 chunk 214 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 56 ASN A 391 HIS B 40 GLN B 56 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS C 56 ASN C 391 HIS D 40 GLN D 56 ASN D 391 HIS E 40 GLN E 56 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 HIS F 56 ASN F 391 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23988 Z= 0.304 Angle : 0.658 10.415 32442 Z= 0.328 Chirality : 0.044 0.179 3516 Planarity : 0.004 0.034 4194 Dihedral : 12.719 162.768 3342 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.96 % Favored : 94.64 % Rotamer: Outliers : 1.40 % Allowed : 7.13 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.62 (0.15), residues: 2964 helix: 0.68 (0.14), residues: 1482 sheet: -1.60 (0.28), residues: 282 loop : -1.46 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 281 HIS 0.003 0.001 HIS F 57 PHE 0.028 0.002 PHE D 360 TYR 0.024 0.002 TYR C 407 ARG 0.003 0.000 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 292 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 384 GLU cc_start: 0.7884 (tt0) cc_final: 0.7631 (tt0) REVERT: B 402 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7533 (mt-10) REVERT: B 421 PHE cc_start: 0.7404 (p90) cc_final: 0.7021 (p90) REVERT: C 181 ASP cc_start: 0.7755 (t0) cc_final: 0.7504 (t0) REVERT: C 421 PHE cc_start: 0.7419 (p90) cc_final: 0.7023 (p90) REVERT: E 384 GLU cc_start: 0.7916 (tt0) cc_final: 0.7671 (tt0) REVERT: E 402 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7530 (mt-10) REVERT: E 421 PHE cc_start: 0.7397 (p90) cc_final: 0.7015 (p90) REVERT: F 181 ASP cc_start: 0.7750 (t0) cc_final: 0.7482 (t0) REVERT: F 421 PHE cc_start: 0.7427 (p90) cc_final: 0.7029 (p90) outliers start: 35 outliers final: 21 residues processed: 315 average time/residue: 0.3091 time to fit residues: 158.9730 Evaluate side-chains 251 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 407 TYR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 407 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 127 optimal weight: 0.2980 chunk 179 optimal weight: 8.9990 chunk 268 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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: 0.8029 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23988 Z= 0.245 Angle : 0.622 9.604 32442 Z= 0.310 Chirality : 0.043 0.167 3516 Planarity : 0.004 0.036 4194 Dihedral : 12.244 154.525 3342 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.28 % Favored : 95.31 % Rotamer: Outliers : 1.68 % Allowed : 9.29 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.06 (0.16), residues: 2964 helix: 1.28 (0.14), residues: 1482 sheet: -1.27 (0.30), residues: 282 loop : -1.18 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 281 HIS 0.004 0.001 HIS B 298 PHE 0.025 0.002 PHE F 247 TYR 0.022 0.002 TYR C 407 ARG 0.003 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 297 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7507 (mt-10) REVERT: B 384 GLU cc_start: 0.7906 (tt0) cc_final: 0.7646 (tt0) REVERT: C 181 ASP cc_start: 0.7777 (t0) cc_final: 0.7440 (t0) REVERT: C 250 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8159 (tm-30) REVERT: D 176 MET cc_start: 0.8840 (mmp) cc_final: 0.8562 (mmp) REVERT: D 402 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7506 (mt-10) REVERT: E 364 ASN cc_start: 0.8372 (t0) cc_final: 0.8104 (t0) REVERT: E 384 GLU cc_start: 0.7906 (tt0) cc_final: 0.7658 (tt0) REVERT: F 181 ASP cc_start: 0.7795 (t0) cc_final: 0.7470 (t0) REVERT: F 250 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8148 (tm-30) outliers start: 42 outliers final: 32 residues processed: 322 average time/residue: 0.3166 time to fit residues: 165.9746 Evaluate side-chains 270 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 238 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 407 TYR Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 211 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 196 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 255 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 40 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN E 40 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23988 Z= 0.306 Angle : 0.660 10.308 32442 Z= 0.328 Chirality : 0.043 0.171 3516 Planarity : 0.004 0.034 4194 Dihedral : 11.412 145.018 3342 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.13 % Favored : 94.47 % Rotamer: Outliers : 1.60 % Allowed : 10.82 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.08 (0.16), residues: 2964 helix: 1.32 (0.14), residues: 1476 sheet: -1.61 (0.27), residues: 336 loop : -1.04 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 281 HIS 0.005 0.001 HIS A 298 PHE 0.028 0.002 PHE E 360 TYR 0.021 0.002 TYR F 407 ARG 0.009 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 266 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.7980 (mmp) cc_final: 0.7690 (mmt) REVERT: A 281 TRP cc_start: 0.7434 (t60) cc_final: 0.7161 (t60) REVERT: A 402 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7653 (mt-10) REVERT: B 250 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8086 (tm-30) REVERT: B 384 GLU cc_start: 0.7957 (tt0) cc_final: 0.7665 (tt0) REVERT: B 402 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 250 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8105 (tm-30) REVERT: D 169 MET cc_start: 0.7984 (mmp) cc_final: 0.7688 (mmt) REVERT: D 402 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7644 (mt-10) REVERT: E 402 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7565 (mt-10) REVERT: F 250 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8069 (tm-30) outliers start: 40 outliers final: 36 residues processed: 284 average time/residue: 0.3159 time to fit residues: 146.7423 Evaluate side-chains 266 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 407 TYR Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 9.9990 chunk 255 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 23988 Z= 0.366 Angle : 0.683 10.936 32442 Z= 0.341 Chirality : 0.044 0.178 3516 Planarity : 0.004 0.034 4194 Dihedral : 10.649 179.654 3342 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.63 % Favored : 93.99 % Rotamer: Outliers : 2.56 % Allowed : 11.58 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.04 (0.16), residues: 2964 helix: 1.28 (0.14), residues: 1476 sheet: -1.36 (0.29), residues: 306 loop : -1.17 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 281 HIS 0.005 0.001 HIS F 450 PHE 0.033 0.002 PHE D 247 TYR 0.021 0.002 TYR F 407 ARG 0.003 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 254 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.7459 (m-10) cc_final: 0.7233 (m-10) REVERT: A 281 TRP cc_start: 0.7380 (t60) cc_final: 0.6966 (t60) REVERT: A 402 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7684 (mt-10) REVERT: B 181 ASP cc_start: 0.7895 (t0) cc_final: 0.7693 (t0) REVERT: B 250 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8089 (tm-30) REVERT: B 384 GLU cc_start: 0.8000 (tt0) cc_final: 0.7747 (tt0) REVERT: C 250 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8093 (tm-30) REVERT: D 63 PHE cc_start: 0.7422 (m-10) cc_final: 0.7201 (m-10) REVERT: D 402 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7677 (mt-10) REVERT: E 250 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8085 (tm-30) REVERT: F 250 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8070 (tm-30) outliers start: 64 outliers final: 40 residues processed: 290 average time/residue: 0.3090 time to fit residues: 148.2379 Evaluate side-chains 267 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 227 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 407 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 407 TYR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 189 HIS Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 407 TYR Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 283 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN C 135 ASN C 387 ASN D 135 ASN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN F 135 ASN F 387 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23988 Z= 0.263 Angle : 0.628 9.498 32442 Z= 0.314 Chirality : 0.043 0.165 3516 Planarity : 0.004 0.035 4194 Dihedral : 10.189 174.965 3342 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.77 % Favored : 94.03 % Rotamer: Outliers : 1.68 % Allowed : 13.14 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2964 helix: 1.42 (0.14), residues: 1470 sheet: -1.31 (0.30), residues: 306 loop : -1.08 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 281 HIS 0.003 0.001 HIS E 450 PHE 0.036 0.002 PHE E 360 TYR 0.021 0.002 TYR F 407 ARG 0.003 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 237 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.8062 (mmp) cc_final: 0.7860 (mmp) REVERT: A 281 TRP cc_start: 0.7246 (t60) cc_final: 0.7004 (t60) REVERT: A 402 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7644 (mt-10) REVERT: B 250 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8075 (tm-30) REVERT: B 384 GLU cc_start: 0.7965 (tt0) cc_final: 0.7718 (tt0) REVERT: C 250 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 402 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7638 (mt-10) REVERT: E 250 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8075 (tm-30) REVERT: F 250 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8016 (tm-30) outliers start: 42 outliers final: 35 residues processed: 258 average time/residue: 0.3027 time to fit residues: 129.4741 Evaluate side-chains 256 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 221 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 407 TYR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 407 TYR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 402 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 140 optimal weight: 0.0370 chunk 26 optimal weight: 30.0000 chunk 222 optimal weight: 20.0000 overall best weight: 3.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23988 Z= 0.213 Angle : 0.607 9.219 32442 Z= 0.304 Chirality : 0.042 0.166 3516 Planarity : 0.004 0.035 4194 Dihedral : 10.056 178.564 3342 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.23 % Favored : 94.60 % Rotamer: Outliers : 1.68 % Allowed : 13.42 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.43 (0.16), residues: 2964 helix: 1.59 (0.14), residues: 1434 sheet: -1.08 (0.31), residues: 276 loop : -0.93 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 281 HIS 0.003 0.001 HIS B 258 PHE 0.033 0.002 PHE E 360 TYR 0.027 0.002 TYR D 310 ARG 0.007 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 236 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.8032 (mmp) cc_final: 0.7830 (mmp) REVERT: A 402 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7626 (mt-10) REVERT: B 250 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8103 (tm-30) REVERT: B 384 GLU cc_start: 0.7957 (tt0) cc_final: 0.7728 (tt0) REVERT: C 250 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7973 (tm-30) REVERT: D 402 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7616 (mt-10) REVERT: E 250 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8094 (tm-30) REVERT: E 402 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7523 (mt-10) REVERT: F 250 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7987 (tm-30) outliers start: 42 outliers final: 31 residues processed: 262 average time/residue: 0.3177 time to fit residues: 138.2635 Evaluate side-chains 248 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 217 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 402 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.9980 chunk 271 optimal weight: 0.0000 chunk 247 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 81 optimal weight: 40.0000 chunk 238 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 263 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23988 Z= 0.190 Angle : 0.596 8.757 32442 Z= 0.298 Chirality : 0.041 0.168 3516 Planarity : 0.004 0.037 4194 Dihedral : 9.961 179.860 3342 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.20 % Favored : 94.64 % Rotamer: Outliers : 1.16 % Allowed : 13.82 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.55 (0.16), residues: 2964 helix: 1.71 (0.14), residues: 1428 sheet: -0.93 (0.32), residues: 276 loop : -0.89 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 281 HIS 0.002 0.001 HIS C 258 PHE 0.031 0.002 PHE F 360 TYR 0.021 0.002 TYR D 407 ARG 0.006 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 252 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7533 (mt-10) REVERT: B 250 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 384 GLU cc_start: 0.7967 (tt0) cc_final: 0.7721 (tt0) REVERT: B 402 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7503 (mt-10) REVERT: C 250 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7937 (tm-30) REVERT: D 314 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8208 (tt) REVERT: D 402 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7517 (mt-10) REVERT: E 250 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8213 (tm-30) REVERT: E 384 GLU cc_start: 0.8316 (tp30) cc_final: 0.8041 (tp30) REVERT: E 402 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7504 (mt-10) REVERT: F 233 MET cc_start: 0.7835 (mmm) cc_final: 0.7612 (mmm) REVERT: F 250 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7991 (tm-30) outliers start: 29 outliers final: 16 residues processed: 272 average time/residue: 0.3192 time to fit residues: 141.4376 Evaluate side-chains 251 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 234 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 6.9990 chunk 279 optimal weight: 50.0000 chunk 170 optimal weight: 0.0270 chunk 132 optimal weight: 50.0000 chunk 194 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 233 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 overall best weight: 4.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN D 205 GLN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23988 Z= 0.248 Angle : 0.633 9.431 32442 Z= 0.316 Chirality : 0.042 0.167 3516 Planarity : 0.004 0.036 4194 Dihedral : 9.928 179.989 3342 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.47 % Favored : 94.33 % Rotamer: Outliers : 0.80 % Allowed : 14.30 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.58 (0.16), residues: 2964 helix: 1.72 (0.14), residues: 1428 sheet: -0.84 (0.32), residues: 276 loop : -0.89 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 281 HIS 0.003 0.001 HIS C 258 PHE 0.032 0.002 PHE C 247 TYR 0.028 0.002 TYR D 310 ARG 0.006 0.000 ARG F 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 235 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.8051 (mmm) cc_final: 0.7816 (mmm) REVERT: A 402 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7556 (mt-10) REVERT: B 250 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 384 GLU cc_start: 0.7988 (tt0) cc_final: 0.7751 (tt0) REVERT: B 402 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7509 (mt-10) REVERT: C 233 MET cc_start: 0.7991 (mmm) cc_final: 0.7640 (mmm) REVERT: D 233 MET cc_start: 0.8054 (mmm) cc_final: 0.7820 (mmm) REVERT: D 314 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8227 (tt) REVERT: D 402 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7551 (mt-10) REVERT: E 250 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8134 (tm-30) REVERT: E 402 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7504 (mt-10) REVERT: F 233 MET cc_start: 0.7950 (mmm) cc_final: 0.7678 (mmm) REVERT: F 250 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8011 (tm-30) outliers start: 20 outliers final: 18 residues processed: 248 average time/residue: 0.3123 time to fit residues: 128.2350 Evaluate side-chains 243 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.097690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.074771 restraints weight = 59583.628| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.73 r_work: 0.3127 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23988 Z= 0.171 Angle : 0.598 9.828 32442 Z= 0.298 Chirality : 0.041 0.167 3516 Planarity : 0.004 0.037 4194 Dihedral : 9.739 177.889 3342 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.82 % Favored : 95.07 % Rotamer: Outliers : 0.64 % Allowed : 14.78 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.16), residues: 2964 helix: 1.81 (0.14), residues: 1428 sheet: -0.85 (0.32), residues: 276 loop : -0.80 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 281 HIS 0.002 0.001 HIS E 258 PHE 0.037 0.002 PHE B 360 TYR 0.023 0.001 TYR D 310 ARG 0.006 0.000 ARG F 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4806.80 seconds wall clock time: 88 minutes 45.46 seconds (5325.46 seconds total)