Starting phenix.real_space_refine on Mon Dec 11 13:11:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/12_2023/6pk4_20354_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/12_2023/6pk4_20354.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/12_2023/6pk4_20354_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/12_2023/6pk4_20354_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/12_2023/6pk4_20354_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/12_2023/6pk4_20354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/12_2023/6pk4_20354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/12_2023/6pk4_20354_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/12_2023/6pk4_20354_updated.pdb" } resolution = 3.5 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= 0.023 sd= 0.773 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 24 5.49 5 S 96 5.16 5 C 11332 2.51 5 N 3084 2.21 5 O 3340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 68": "OD1" <-> "OD2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 68": "OD1" <-> "OD2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17876 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "B" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "C" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "D" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU A 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU A 155 " occ=0.75 residue: pdb=" N CYS A 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS A 243 " occ=0.75 residue: pdb=" N GLU B 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU B 155 " occ=0.75 residue: pdb=" N CYS B 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 243 " occ=0.75 residue: pdb=" N GLU C 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU C 155 " occ=0.75 residue: pdb=" N CYS C 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS C 243 " occ=0.75 residue: pdb=" N GLU D 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU D 155 " occ=0.75 residue: pdb=" N CYS D 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS D 243 " occ=0.75 Time building chain proxies: 10.09, per 1000 atoms: 0.56 Number of scatterers: 17876 At special positions: 0 Unit cell: (137.55, 87.15, 124.95, 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 96 16.00 P 24 15.00 O 3340 8.00 N 3084 7.00 C 11332 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.82 Conformation dependent library (CDL) restraints added in 3.3 seconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 24 sheets defined 37.4% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.606A pdb=" N SER A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.502A pdb=" N ASN A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 100 " --> pdb=" O HIS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 116 No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 118 through 130 removed outlier: 4.044A pdb=" N MET A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 Proline residue: A 158 - end of helix removed outlier: 4.576A pdb=" N GLU A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN A 165 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 169 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 195 through 207 removed outlier: 3.539A pdb=" N GLY A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 251 through 259 removed outlier: 4.023A pdb=" N VAL A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 269 removed outlier: 3.899A pdb=" N LYS A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 removed outlier: 3.656A pdb=" N ASP A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 removed outlier: 4.356A pdb=" N ALA A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.891A pdb=" N GLU A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 removed outlier: 4.781A pdb=" N GLN A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 412 removed outlier: 3.619A pdb=" N VAL A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.703A pdb=" N LEU A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.503A pdb=" N GLN A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 547 removed outlier: 3.615A pdb=" N GLY A 542 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 557 removed outlier: 3.674A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 removed outlier: 3.607A pdb=" N SER B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 90 through 101 removed outlier: 3.502A pdb=" N ASN B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 100 " --> pdb=" O HIS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 118 through 130 removed outlier: 4.044A pdb=" N MET B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 169 Proline residue: B 158 - end of helix removed outlier: 4.577A pdb=" N GLU B 161 " --> pdb=" O PRO B 158 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN B 165 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 169 " --> pdb=" O PHE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 195 through 207 removed outlier: 3.538A pdb=" N GLY B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 251 through 259 removed outlier: 4.023A pdb=" N VAL B 255 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 269 removed outlier: 3.899A pdb=" N LYS B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 3.656A pdb=" N ASP B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 327 removed outlier: 4.357A pdb=" N ALA B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.892A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 390 removed outlier: 4.781A pdb=" N GLN B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 412 removed outlier: 3.619A pdb=" N VAL B 406 " --> pdb=" O MET B 402 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 removed outlier: 3.702A pdb=" N LEU B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.503A pdb=" N GLN B 491 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 547 removed outlier: 3.615A pdb=" N GLY B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 removed outlier: 3.674A pdb=" N LEU B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 removed outlier: 3.606A pdb=" N SER C 22 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.501A pdb=" N ASN C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS C 100 " --> pdb=" O HIS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 116 No H-bonds generated for 'chain 'C' and resid 113 through 116' Processing helix chain 'C' and resid 118 through 130 removed outlier: 4.044A pdb=" N MET C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 169 Proline residue: C 158 - end of helix removed outlier: 4.577A pdb=" N GLU C 161 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN C 165 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 169 " --> pdb=" O PHE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 195 through 207 removed outlier: 3.538A pdb=" N GLY C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 251 through 259 removed outlier: 4.022A pdb=" N VAL C 255 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 269 removed outlier: 3.899A pdb=" N LYS C 267 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 3.656A pdb=" N ASP C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 292 " --> pdb=" O MET C 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 removed outlier: 4.357A pdb=" N ALA C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 349 Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.891A pdb=" N GLU C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 390 removed outlier: 4.781A pdb=" N GLN C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 412 removed outlier: 3.619A pdb=" N VAL C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 410 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 removed outlier: 3.703A pdb=" N LEU C 467 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 3.503A pdb=" N GLN C 491 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 547 removed outlier: 3.614A pdb=" N GLY C 542 " --> pdb=" O PRO C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 557 removed outlier: 3.674A pdb=" N LEU C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.606A pdb=" N SER D 22 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.501A pdb=" N ASN D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS D 100 " --> pdb=" O HIS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 116 No H-bonds generated for 'chain 'D' and resid 113 through 116' Processing helix chain 'D' and resid 118 through 130 removed outlier: 4.045A pdb=" N MET D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 169 Proline residue: D 158 - end of helix removed outlier: 4.577A pdb=" N GLU D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN D 165 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS D 169 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 195 through 207 removed outlier: 3.539A pdb=" N GLY D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 251 through 259 removed outlier: 4.023A pdb=" N VAL D 255 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU D 258 " --> pdb=" O PRO D 254 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 269 removed outlier: 3.899A pdb=" N LYS D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 removed outlier: 3.656A pdb=" N ASP D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 292 " --> pdb=" O MET D 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 327 removed outlier: 4.357A pdb=" N ALA D 320 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.892A pdb=" N GLU D 356 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 390 removed outlier: 4.780A pdb=" N GLN D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 412 removed outlier: 3.619A pdb=" N VAL D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 410 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 removed outlier: 3.703A pdb=" N LEU D 467 " --> pdb=" O ILE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.503A pdb=" N GLN D 491 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 547 removed outlier: 3.614A pdb=" N GLY D 542 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 557 removed outlier: 3.674A pdb=" N LEU D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 175 through 177 removed outlier: 6.718A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 35 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 182 removed outlier: 6.201A pdb=" N VAL A 215 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 303 through 305 Processing sheet with id= D, first strand: chain 'A' and resid 367 through 369 removed outlier: 3.831A pdb=" N LEU A 396 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE A 520 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 522 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 513 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 482 through 484 removed outlier: 3.501A pdb=" N ASP A 420 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 473 through 480 removed outlier: 3.862A pdb=" N HIS A 478 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 451 " --> pdb=" O HIS A 478 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 480 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 449 " --> pdb=" O HIS A 480 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.718A pdb=" N TYR B 3 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 35 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 180 through 182 removed outlier: 6.200A pdb=" N VAL B 215 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 303 through 305 Processing sheet with id= J, first strand: chain 'B' and resid 367 through 369 removed outlier: 3.831A pdb=" N LEU B 396 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE B 520 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 522 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 513 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 482 through 484 removed outlier: 3.501A pdb=" N ASP B 420 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 473 through 480 removed outlier: 3.861A pdb=" N HIS B 478 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 451 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS B 480 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 449 " --> pdb=" O HIS B 480 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.718A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 35 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 180 through 182 removed outlier: 6.201A pdb=" N VAL C 215 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 303 through 305 Processing sheet with id= P, first strand: chain 'C' and resid 367 through 369 removed outlier: 3.832A pdb=" N LEU C 396 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 522 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 513 " --> pdb=" O SER C 498 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 482 through 484 removed outlier: 3.501A pdb=" N ASP C 420 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 473 through 480 removed outlier: 3.861A pdb=" N HIS C 478 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY C 451 " --> pdb=" O HIS C 478 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 480 " --> pdb=" O ARG C 449 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 449 " --> pdb=" O HIS C 480 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 175 through 177 removed outlier: 6.718A pdb=" N TYR D 3 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 35 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 180 through 182 removed outlier: 6.201A pdb=" N VAL D 215 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 303 through 305 Processing sheet with id= V, first strand: chain 'D' and resid 367 through 369 removed outlier: 3.832A pdb=" N LEU D 396 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE D 520 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 522 " --> pdb=" O ILE D 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 513 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 482 through 484 removed outlier: 3.501A pdb=" N ASP D 420 " --> pdb=" O VAL D 430 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 473 through 480 removed outlier: 3.861A pdb=" N HIS D 478 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY D 451 " --> pdb=" O HIS D 478 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS D 480 " --> pdb=" O ARG D 449 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 449 " --> pdb=" O HIS D 480 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 2726 1.25 - 1.39: 4536 1.39 - 1.53: 10173 1.53 - 1.68: 673 1.68 - 1.82: 152 Bond restraints: 18260 Sorted by residual: bond pdb=" C4' UTP A 601 " pdb=" O4' UTP A 601 " ideal model delta sigma weight residual 1.320 1.534 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C4' UTP C 601 " pdb=" O4' UTP C 601 " ideal model delta sigma weight residual 1.320 1.534 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C4' UTP D 601 " pdb=" O4' UTP D 601 " ideal model delta sigma weight residual 1.320 1.533 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C4' UTP B 601 " pdb=" O4' UTP B 601 " ideal model delta sigma weight residual 1.320 1.533 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C1' UTP D 601 " pdb=" O4' UTP D 601 " ideal model delta sigma weight residual 1.553 1.351 0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 18255 not shown) Histogram of bond angle deviations from ideal: 97.54 - 105.84: 564 105.84 - 114.14: 10544 114.14 - 122.45: 11026 122.45 - 130.75: 2526 130.75 - 139.05: 100 Bond angle restraints: 24760 Sorted by residual: angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 120.55 19.32 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 120.58 19.29 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 120.60 19.27 1.00e+00 1.00e+00 3.71e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 120.61 19.26 1.00e+00 1.00e+00 3.71e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 120.57 16.26 1.00e+00 1.00e+00 2.64e+02 ... (remaining 24755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 10296 16.92 - 33.84: 568 33.84 - 50.75: 176 50.75 - 67.67: 36 67.67 - 84.59: 4 Dihedral angle restraints: 11080 sinusoidal: 4660 harmonic: 6420 Sorted by residual: dihedral pdb=" CA VAL B 58 " pdb=" C VAL B 58 " pdb=" N PHE B 59 " pdb=" CA PHE B 59 " ideal model delta harmonic sigma weight residual 180.00 136.26 43.74 0 5.00e+00 4.00e-02 7.65e+01 dihedral pdb=" CA VAL C 58 " pdb=" C VAL C 58 " pdb=" N PHE C 59 " pdb=" CA PHE C 59 " ideal model delta harmonic sigma weight residual 180.00 136.29 43.71 0 5.00e+00 4.00e-02 7.64e+01 dihedral pdb=" CA VAL D 58 " pdb=" C VAL D 58 " pdb=" N PHE D 59 " pdb=" CA PHE D 59 " ideal model delta harmonic sigma weight residual 180.00 136.31 43.69 0 5.00e+00 4.00e-02 7.64e+01 ... (remaining 11077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2587 0.137 - 0.274: 121 0.274 - 0.411: 28 0.411 - 0.548: 8 0.548 - 0.685: 8 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CB ILE B 301 " pdb=" CA ILE B 301 " pdb=" CG1 ILE B 301 " pdb=" CG2 ILE B 301 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CB ILE D 301 " pdb=" CA ILE D 301 " pdb=" CG1 ILE D 301 " pdb=" CG2 ILE D 301 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CB ILE A 301 " pdb=" CA ILE A 301 " pdb=" CG1 ILE A 301 " pdb=" CG2 ILE A 301 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 2749 not shown) Planarity restraints: 3172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 66 " 0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU A 66 " -0.088 2.00e-02 2.50e+03 pdb=" O GLU A 66 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL A 67 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 66 " -0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU D 66 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU D 66 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL D 67 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 66 " -0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU C 66 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU C 66 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL C 67 " -0.029 2.00e-02 2.50e+03 ... (remaining 3169 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 40 2.08 - 2.79: 4513 2.79 - 3.49: 23299 3.49 - 4.20: 41898 4.20 - 4.90: 71259 Nonbonded interactions: 141009 Sorted by model distance: nonbonded pdb=" O LEU B 69 " pdb=" N LEU B 71 " model vdw 1.380 2.520 nonbonded pdb=" O LEU A 69 " pdb=" N LEU A 71 " model vdw 1.381 2.520 nonbonded pdb=" O LEU D 69 " pdb=" N LEU D 71 " model vdw 1.381 2.520 nonbonded pdb=" O LEU C 69 " pdb=" N LEU C 71 " model vdw 1.381 2.520 nonbonded pdb=" OD1 ASP A 70 " pdb=" O1B ATP A 602 " model vdw 1.413 3.040 ... (remaining 141004 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' } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 6.680 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 48.140 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 0.011 0.214 18260 Z= 0.721 Angle : 1.371 19.319 24760 Z= 0.817 Chirality : 0.085 0.685 2752 Planarity : 0.009 0.072 3172 Dihedral : 12.048 84.590 6960 Min Nonbonded Distance : 1.380 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.54 % Favored : 91.56 % Rotamer: Outliers : 1.44 % Allowed : 5.35 % Favored : 93.21 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 1.13 % 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: -4.81 (0.14), residues: 2228 helix: -3.89 (0.11), residues: 768 sheet: -3.32 (0.22), residues: 380 loop : -2.47 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 124 HIS 0.007 0.002 HIS A 235 PHE 0.033 0.003 PHE A 482 TYR 0.058 0.005 TYR B 94 ARG 0.008 0.001 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 492 time to evaluate : 2.109 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 outliers start: 28 outliers final: 20 residues processed: 516 average time/residue: 0.3465 time to fit residues: 258.7031 Evaluate side-chains 246 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 2.179 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 4 residues processed: 20 average time/residue: 0.1629 time to fit residues: 8.8659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 99 ASN A 192 GLN B 95 GLN B 99 ASN B 192 GLN C 95 GLN C 99 ASN C 192 GLN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 99 ASN D 192 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18260 Z= 0.249 Angle : 0.774 9.430 24760 Z= 0.402 Chirality : 0.056 0.680 2752 Planarity : 0.007 0.059 3172 Dihedral : 10.396 86.674 2588 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.01 % Favored : 93.72 % Rotamer: Outliers : 4.01 % Allowed : 13.01 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -3.64 (0.15), residues: 2228 helix: -2.49 (0.15), residues: 828 sheet: -2.60 (0.24), residues: 360 loop : -2.15 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 124 HIS 0.006 0.001 HIS D 55 PHE 0.019 0.002 PHE A 520 TYR 0.018 0.002 TYR D 53 ARG 0.012 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 267 time to evaluate : 2.195 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 outliers start: 78 outliers final: 25 residues processed: 314 average time/residue: 0.3004 time to fit residues: 144.7241 Evaluate side-chains 247 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 1.964 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 4 residues processed: 25 average time/residue: 0.1721 time to fit residues: 10.3520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 136 optimal weight: 0.4980 chunk 55 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18260 Z= 0.237 Angle : 0.701 8.528 24760 Z= 0.360 Chirality : 0.047 0.245 2752 Planarity : 0.005 0.057 3172 Dihedral : 9.702 81.294 2588 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.01 % Favored : 93.81 % Rotamer: Outliers : 3.40 % Allowed : 14.25 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.92 (0.16), residues: 2228 helix: -1.65 (0.16), residues: 848 sheet: -2.34 (0.25), residues: 348 loop : -1.91 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 124 HIS 0.004 0.001 HIS A 330 PHE 0.021 0.002 PHE B 520 TYR 0.017 0.002 TYR A 106 ARG 0.006 0.001 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 252 time to evaluate : 2.066 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 outliers start: 66 outliers final: 17 residues processed: 312 average time/residue: 0.3069 time to fit residues: 148.1292 Evaluate side-chains 238 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 2.013 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 17 average time/residue: 0.1745 time to fit residues: 8.4127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 190 optimal weight: 0.0040 chunk 57 optimal weight: 4.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 192 GLN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS B 192 GLN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN C 323 HIS C 526 HIS D 192 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18260 Z= 0.204 Angle : 0.682 8.963 24760 Z= 0.340 Chirality : 0.046 0.193 2752 Planarity : 0.005 0.056 3172 Dihedral : 9.476 85.150 2588 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.21 % Favored : 94.61 % Rotamer: Outliers : 3.19 % Allowed : 16.87 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -2.56 (0.17), residues: 2228 helix: -1.11 (0.18), residues: 848 sheet: -2.40 (0.25), residues: 364 loop : -1.82 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 124 HIS 0.005 0.001 HIS D 330 PHE 0.022 0.002 PHE B 409 TYR 0.012 0.002 TYR A 106 ARG 0.005 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 249 time to evaluate : 1.962 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: 62 outliers final: 35 residues processed: 294 average time/residue: 0.2939 time to fit residues: 134.5139 Evaluate side-chains 249 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 214 time to evaluate : 2.039 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 4 residues processed: 35 average time/residue: 0.1798 time to fit residues: 14.4328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS D 116 HIS ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18260 Z= 0.237 Angle : 0.687 7.971 24760 Z= 0.343 Chirality : 0.047 0.202 2752 Planarity : 0.005 0.056 3172 Dihedral : 9.233 88.410 2588 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.21 % Favored : 94.61 % Rotamer: Outliers : 1.85 % Allowed : 18.11 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -2.25 (0.17), residues: 2228 helix: -0.82 (0.18), residues: 848 sheet: -2.32 (0.25), residues: 364 loop : -1.65 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 124 HIS 0.003 0.001 HIS B 116 PHE 0.027 0.002 PHE B 520 TYR 0.015 0.002 TYR B 468 ARG 0.004 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 2.099 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 outliers start: 36 outliers final: 24 residues processed: 262 average time/residue: 0.2795 time to fit residues: 114.8819 Evaluate side-chains 226 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 2.350 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 4 residues processed: 24 average time/residue: 0.1788 time to fit residues: 10.9655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 42 optimal weight: 0.2980 chunk 124 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 176 optimal weight: 0.2980 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 323 HIS B 167 GLN B 323 HIS C 167 GLN D 167 GLN D 323 HIS ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18260 Z= 0.193 Angle : 0.679 16.400 24760 Z= 0.333 Chirality : 0.046 0.201 2752 Planarity : 0.004 0.055 3172 Dihedral : 8.874 82.449 2588 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.21 % Favored : 94.61 % Rotamer: Outliers : 1.65 % Allowed : 18.83 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -2.06 (0.17), residues: 2228 helix: -0.57 (0.18), residues: 844 sheet: -2.24 (0.25), residues: 368 loop : -1.60 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 124 HIS 0.003 0.001 HIS D 480 PHE 0.023 0.001 PHE C 520 TYR 0.010 0.001 TYR C 468 ARG 0.003 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 2.159 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: 32 outliers final: 24 residues processed: 235 average time/residue: 0.3028 time to fit residues: 111.5198 Evaluate side-chains 226 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 2.010 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 4 residues processed: 24 average time/residue: 0.1783 time to fit residues: 10.6687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 120 optimal weight: 0.0570 chunk 179 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.1904 ------------------------------------------------------------------------------- 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: 0.7635 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18260 Z= 0.239 Angle : 0.692 10.937 24760 Z= 0.339 Chirality : 0.047 0.246 2752 Planarity : 0.004 0.054 3172 Dihedral : 8.533 81.052 2588 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.08 % Allowed : 20.37 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -1.84 (0.18), residues: 2228 helix: -0.43 (0.18), residues: 840 sheet: -2.02 (0.26), residues: 356 loop : -1.50 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 124 HIS 0.003 0.001 HIS C 116 PHE 0.016 0.001 PHE D 520 TYR 0.011 0.002 TYR C 468 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 2.990 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 outliers start: 21 outliers final: 9 residues processed: 213 average time/residue: 0.3347 time to fit residues: 111.2292 Evaluate side-chains 202 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 2.027 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 9 average time/residue: 0.1990 time to fit residues: 5.9936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 104 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 192 optimal weight: 30.0000 overall best weight: 1.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN B 443 ASN C 443 ASN D 443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18260 Z= 0.188 Angle : 0.692 12.902 24760 Z= 0.335 Chirality : 0.046 0.248 2752 Planarity : 0.004 0.053 3172 Dihedral : 8.266 80.425 2588 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.08 % Allowed : 21.14 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -1.52 (0.18), residues: 2228 helix: -0.18 (0.19), residues: 824 sheet: -1.96 (0.26), residues: 348 loop : -1.24 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 124 HIS 0.003 0.001 HIS C 330 PHE 0.019 0.001 PHE A 520 TYR 0.010 0.001 TYR C 42 ARG 0.003 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 2.066 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: 21 outliers final: 18 residues processed: 236 average time/residue: 0.2976 time to fit residues: 110.3396 Evaluate side-chains 216 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 2.008 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 18 average time/residue: 0.1806 time to fit residues: 8.6230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 87 ASN C 87 ASN D 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18260 Z= 0.257 Angle : 0.707 9.665 24760 Z= 0.350 Chirality : 0.047 0.212 2752 Planarity : 0.004 0.053 3172 Dihedral : 8.159 81.596 2588 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.57 % Allowed : 21.91 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -1.49 (0.18), residues: 2228 helix: -0.15 (0.19), residues: 816 sheet: -1.81 (0.26), residues: 356 loop : -1.27 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 124 HIS 0.003 0.001 HIS A 526 PHE 0.026 0.002 PHE A 520 TYR 0.013 0.002 TYR C 468 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 2.228 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: 11 outliers final: 7 residues processed: 217 average time/residue: 0.2966 time to fit residues: 98.8790 Evaluate side-chains 200 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 2.047 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 7 average time/residue: 0.1805 time to fit residues: 5.0349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 145 optimal weight: 0.0270 chunk 219 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 overall best weight: 1.7840 ------------------------------------------------------------------------------- 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: 0.7626 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18260 Z= 0.231 Angle : 0.726 11.455 24760 Z= 0.356 Chirality : 0.047 0.211 2752 Planarity : 0.004 0.053 3172 Dihedral : 8.012 82.003 2588 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.31 % Allowed : 22.27 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -1.30 (0.18), residues: 2228 helix: -0.13 (0.19), residues: 824 sheet: -1.47 (0.27), residues: 332 loop : -1.17 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 124 HIS 0.004 0.001 HIS B 526 PHE 0.023 0.002 PHE C 520 TYR 0.011 0.002 TYR D 468 ARG 0.003 0.000 ARG C 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 192 time to evaluate : 2.034 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: 6 outliers final: 5 residues processed: 198 average time/residue: 0.3029 time to fit residues: 93.0545 Evaluate side-chains 194 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 189 time to evaluate : 2.108 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 5 average time/residue: 0.1821 time to fit residues: 4.5488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.0050 chunk 53 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 73 optimal weight: 0.0050 chunk 179 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 153 optimal weight: 0.2980 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.127013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.102397 restraints weight = 39121.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.106336 restraints weight = 20228.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109034 restraints weight = 13132.274| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18260 Z= 0.184 Angle : 0.704 11.803 24760 Z= 0.342 Chirality : 0.046 0.206 2752 Planarity : 0.004 0.052 3172 Dihedral : 7.715 81.065 2588 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.46 % Allowed : 22.07 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -1.26 (0.18), residues: 2228 helix: -0.05 (0.19), residues: 820 sheet: -1.39 (0.27), residues: 336 loop : -1.19 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 285 HIS 0.004 0.001 HIS A 480 PHE 0.019 0.001 PHE C 520 TYR 0.010 0.001 TYR D 307 ARG 0.004 0.000 ARG B 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3451.14 seconds wall clock time: 64 minutes 11.91 seconds (3851.91 seconds total)