Starting phenix.real_space_refine (version: dev) on Fri Feb 24 16:47:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/02_2023/3jd0_6631_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/02_2023/3jd0_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_6631/02_2023/3jd0_6631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/02_2023/3jd0_6631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/02_2023/3jd0_6631_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd0_6631/02_2023/3jd0_6631_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 12.84, per 1000 atoms: 0.55 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: 10.28 Conformation dependent library (CDL) restraints added in 3.4 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: 2.45 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: 7.52 Time building geometry restraints manager: 11.01 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 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. 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: 0.010 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: 5.740 Check model and map are aligned: 0.350 Process input model: 60.930 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 % 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 *********************** 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 : 2.767 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 outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.4141 time to fit residues: 325.2391 Evaluate side-chains 257 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6738 ------------------------------------------------------------------------------- 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: 0.8175 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 23988 Z= 0.307 Angle : 0.713 10.473 32442 Z= 0.361 Chirality : 0.045 0.173 3516 Planarity : 0.005 0.041 4194 Dihedral : 13.128 169.610 3342 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.67 % Favored : 94.13 % Rotamer Outliers : 1.28 % 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: -2.51 (0.14), residues: 2964 helix: -1.15 (0.12), residues: 1506 sheet: -1.93 (0.24), residues: 330 loop : -2.11 (0.16), residues: 1128 *********************** 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 351 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 319 time to evaluate : 2.636 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 outliers start: 32 outliers final: 22 residues processed: 341 average time/residue: 0.3191 time to fit residues: 177.7335 Evaluate side-chains 251 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 2.774 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2018 time to fit residues: 12.2086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 181 optimal weight: 50.0000 chunk 73 optimal weight: 0.0270 chunk 267 optimal weight: 4.9990 chunk 288 optimal weight: 10.0000 chunk 238 optimal weight: 30.0000 chunk 265 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 214 optimal weight: 9.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS B 40 GLN B 56 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN B 391 HIS C 56 ASN ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 56 ASN ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN E 56 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN E 391 HIS F 56 ASN ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 23988 Z= 0.287 Angle : 0.643 10.418 32442 Z= 0.322 Chirality : 0.044 0.179 3516 Planarity : 0.004 0.035 4194 Dihedral : 12.772 163.767 3342 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.89 % Favored : 94.70 % Rotamer Outliers : 1.08 % 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: -0.59 (0.15), residues: 2964 helix: 0.70 (0.14), residues: 1482 sheet: -1.60 (0.28), residues: 282 loop : -1.42 (0.17), residues: 1200 *********************** 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 325 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 298 time to evaluate : 2.832 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 outliers start: 27 outliers final: 10 residues processed: 308 average time/residue: 0.3244 time to fit residues: 162.9433 Evaluate side-chains 248 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 238 time to evaluate : 2.712 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2396 time to fit residues: 7.8943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 254 optimal weight: 5.9990 chunk 76 optimal weight: 40.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** C 391 HIS D 391 HIS F 391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 23988 Z= 0.276 Angle : 0.636 10.009 32442 Z= 0.318 Chirality : 0.043 0.176 3516 Planarity : 0.004 0.036 4194 Dihedral : 12.324 156.359 3342 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.59 % Favored : 95.01 % Rotamer Outliers : 1.36 % 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: 1.24 (0.14), residues: 1482 sheet: -1.31 (0.29), residues: 282 loop : -1.15 (0.17), residues: 1200 *********************** 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 307 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 273 time to evaluate : 2.733 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 outliers start: 34 outliers final: 24 residues processed: 287 average time/residue: 0.3215 time to fit residues: 152.4006 Evaluate side-chains 262 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2180 time to fit residues: 13.4211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 242 optimal weight: 20.0000 chunk 196 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 145 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 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 56 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 23988 Z= 0.309 Angle : 0.660 10.251 32442 Z= 0.329 Chirality : 0.043 0.171 3516 Planarity : 0.004 0.035 4194 Dihedral : 11.592 141.940 3342 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.89 % Favored : 94.70 % Rotamer Outliers : 0.68 % 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: 0.11 (0.16), residues: 2964 helix: 1.32 (0.14), residues: 1476 sheet: -1.60 (0.27), residues: 336 loop : -0.99 (0.18), residues: 1152 *********************** 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 285 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 268 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 277 average time/residue: 0.3270 time to fit residues: 149.3195 Evaluate side-chains 227 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 222 time to evaluate : 2.753 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2446 time to fit residues: 6.0267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN C 135 ASN D 135 ASN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN F 135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 23988 Z= 0.236 Angle : 0.620 8.632 32442 Z= 0.309 Chirality : 0.042 0.161 3516 Planarity : 0.004 0.046 4194 Dihedral : 10.679 179.902 3342 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.42 % Favored : 95.34 % Rotamer Outliers : 0.96 % 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: 0.34 (0.16), residues: 2964 helix: 1.44 (0.14), residues: 1476 sheet: -1.00 (0.27), residues: 396 loop : -0.92 (0.19), residues: 1092 *********************** 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 282 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 258 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 268 average time/residue: 0.3338 time to fit residues: 146.0031 Evaluate side-chains 240 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 224 time to evaluate : 2.781 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2260 time to fit residues: 10.4674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 1.9990 chunk 32 optimal weight: 40.0000 chunk 162 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 chunk 158 optimal weight: 0.4980 chunk 283 optimal weight: 0.7980 chunk 177 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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: 0.8200 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23988 Z= 0.206 Angle : 0.598 8.379 32442 Z= 0.298 Chirality : 0.042 0.156 3516 Planarity : 0.004 0.036 4194 Dihedral : 10.095 173.858 3342 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.14 % Rotamer Outliers : 0.44 % 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: 0.46 (0.16), residues: 2964 helix: 1.49 (0.14), residues: 1476 sheet: -0.43 (0.29), residues: 336 loop : -1.00 (0.18), residues: 1152 *********************** 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 255 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 252 average time/residue: 0.3271 time to fit residues: 135.6676 Evaluate side-chains 227 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 2.536 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2249 time to fit residues: 4.5481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 140 optimal weight: 0.0170 chunk 26 optimal weight: 10.0000 chunk 222 optimal weight: 0.0470 overall best weight: 1.8120 ------------------------------------------------------------------------------- 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: 0.8170 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= 0.177 Angle : 0.589 8.427 32442 Z= 0.294 Chirality : 0.041 0.168 3516 Planarity : 0.004 0.037 4194 Dihedral : 10.040 179.957 3342 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.80 % Rotamer Outliers : 0.24 % 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: 0.69 (0.16), residues: 2964 helix: 1.69 (0.14), residues: 1434 sheet: -0.34 (0.29), residues: 336 loop : -0.82 (0.18), residues: 1194 *********************** 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 258 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 252 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 257 average time/residue: 0.3310 time to fit residues: 140.2474 Evaluate side-chains 237 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 2.869 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2212 time to fit residues: 4.4238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 9.9990 chunk 271 optimal weight: 30.0000 chunk 247 optimal weight: 5.9990 chunk 264 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 238 optimal weight: 20.0000 chunk 249 optimal weight: 4.9990 chunk 263 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 205 GLN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 23988 Z= 0.284 Angle : 0.640 10.322 32442 Z= 0.318 Chirality : 0.042 0.164 3516 Planarity : 0.004 0.036 4194 Dihedral : 9.990 179.674 3342 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.40 % Favored : 94.40 % Rotamer Outliers : 0.48 % 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: 0.63 (0.16), residues: 2964 helix: 1.68 (0.14), residues: 1428 sheet: -0.28 (0.29), residues: 336 loop : -0.91 (0.18), residues: 1200 *********************** 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 247 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 235 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 242 average time/residue: 0.3218 time to fit residues: 129.4344 Evaluate side-chains 223 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 218 time to evaluate : 2.697 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2042 time to fit residues: 5.5577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 7.9990 chunk 279 optimal weight: 0.2980 chunk 170 optimal weight: 0.9980 chunk 132 optimal weight: 40.0000 chunk 194 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 269 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5594 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= 0.219 Angle : 0.605 8.498 32442 Z= 0.302 Chirality : 0.042 0.162 3516 Planarity : 0.004 0.037 4194 Dihedral : 9.898 179.778 3342 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.23 % Favored : 94.67 % Rotamer Outliers : 0.16 % 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: 0.65 (0.16), residues: 2964 helix: 1.71 (0.14), residues: 1428 sheet: -0.29 (0.30), residues: 336 loop : -0.91 (0.18), residues: 1200 ********************** 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 234 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 230 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 234 average time/residue: 0.3510 time to fit residues: 135.5231 Evaluate side-chains 219 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 2.943 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2233 time to fit residues: 4.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 71 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.095148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072150 restraints weight = 60099.692| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.75 r_work: 0.3066 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 23988 Z= 0.223 Angle : 0.609 8.998 32442 Z= 0.304 Chirality : 0.042 0.162 3516 Planarity : 0.004 0.037 4194 Dihedral : 9.815 178.744 3342 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.96 % Favored : 94.91 % Rotamer Outliers : 0.12 % 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: 0.69 (0.16), residues: 2964 helix: 1.73 (0.14), residues: 1428 sheet: -0.24 (0.30), residues: 336 loop : -0.89 (0.18), residues: 1200 =============================================================================== Job complete usr+sys time: 4382.72 seconds wall clock time: 82 minutes 7.33 seconds (4927.33 seconds total)