Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 17:32:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1w_32951/10_2023/7x1w_32951_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1w_32951/10_2023/7x1w_32951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1w_32951/10_2023/7x1w_32951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1w_32951/10_2023/7x1w_32951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1w_32951/10_2023/7x1w_32951_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1w_32951/10_2023/7x1w_32951_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 6 5.49 5 S 44 5.16 5 C 5967 2.51 5 N 1641 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B ARG 622": "NH1" <-> "NH2" Residue "B TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 629": "OD1" <-> "OD2" Residue "B ASP 638": "OD1" <-> "OD2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 674": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 9315 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4624 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 557} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4629 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 558} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.26, per 1000 atoms: 0.56 Number of scatterers: 9315 At special positions: 0 Unit cell: (80.51, 83.83, 135.29, 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 44 16.00 P 6 15.00 O 1657 8.00 N 1641 7.00 C 5967 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: 3.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 3 sheets defined 62.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.808A pdb=" N GLN A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 123 removed outlier: 3.649A pdb=" N TYR A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 174 removed outlier: 3.552A pdb=" N ALA A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 3.537A pdb=" N ARG A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.086A pdb=" N SER A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 235 removed outlier: 3.819A pdb=" N ASP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.649A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 263 through 288 removed outlier: 3.642A pdb=" N GLU A 267 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 288 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 299 through 323 removed outlier: 3.572A pdb=" N ALA A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.872A pdb=" N LEU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 374 through 431 removed outlier: 3.926A pdb=" N SER A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.912A pdb=" N PHE A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 555 No H-bonds generated for 'chain 'A' and resid 553 through 555' Processing helix chain 'A' and resid 575 through 582 Processing helix chain 'A' and resid 586 through 590 removed outlier: 3.663A pdb=" N GLN A 590 " --> pdb=" O HIS A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 586 through 590' Processing helix chain 'A' and resid 607 through 621 removed outlier: 4.252A pdb=" N GLN A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A 612 " --> pdb=" O GLY A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 removed outlier: 3.542A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 removed outlier: 4.028A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 82 removed outlier: 3.712A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 123 removed outlier: 3.645A pdb=" N TYR B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 174 removed outlier: 3.590A pdb=" N ALA B 141 " --> pdb=" O TRP B 137 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix removed outlier: 3.580A pdb=" N ARG B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.049A pdb=" N SER B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 196 No H-bonds generated for 'chain 'B' and resid 193 through 196' Processing helix chain 'B' and resid 199 through 225 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 228 through 235 Processing helix chain 'B' and resid 242 through 288 removed outlier: 3.786A pdb=" N PHE B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Proline residue: B 263 - end of helix removed outlier: 4.744A pdb=" N GLY B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 267 " --> pdb=" O PRO B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 299 through 336 Processing helix chain 'B' and resid 339 through 353 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 374 through 430 removed outlier: 3.931A pdb=" N SER B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.678A pdb=" N GLN B 590 " --> pdb=" O HIS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'B' and resid 607 through 621 removed outlier: 4.129A pdb=" N GLN B 611 " --> pdb=" O GLY B 607 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 removed outlier: 3.855A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 666 removed outlier: 4.219A pdb=" N LYS B 665 " --> pdb=" O SER B 662 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 466 through 469 Processing sheet with id= B, first strand: chain 'A' and resid 540 through 542 Processing sheet with id= C, first strand: chain 'B' and resid 466 through 469 519 hydrogen bonds defined for protein. 1470 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: 2.53 Time building geometry restraints manager: 4.14 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: 3033 1.34 - 1.46: 1597 1.46 - 1.57: 4807 1.57 - 1.69: 12 1.69 - 1.81: 74 Bond restraints: 9523 Sorted by residual: bond pdb=" C2' ATP B 801 " pdb=" C3' ATP B 801 " ideal model delta sigma weight residual 1.531 1.306 0.225 1.20e-02 6.94e+03 3.51e+02 bond pdb=" C2' ATP A 801 " pdb=" C3' ATP A 801 " ideal model delta sigma weight residual 1.531 1.307 0.224 1.20e-02 6.94e+03 3.50e+02 bond pdb=" C4' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.444 1.302 0.142 1.10e-02 8.26e+03 1.67e+02 bond pdb=" C4' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.444 1.302 0.142 1.10e-02 8.26e+03 1.67e+02 bond pdb=" C6 ATP B 801 " pdb=" N6 ATP B 801 " ideal model delta sigma weight residual 1.337 1.465 -0.128 1.10e-02 8.26e+03 1.35e+02 ... (remaining 9518 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.40: 335 107.40 - 114.44: 5529 114.44 - 121.48: 4973 121.48 - 128.52: 1978 128.52 - 135.56: 92 Bond angle restraints: 12907 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 125.41 14.46 1.00e+00 1.00e+00 2.09e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 125.44 14.43 1.00e+00 1.00e+00 2.08e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 124.21 12.62 1.00e+00 1.00e+00 1.59e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 124.29 12.54 1.00e+00 1.00e+00 1.57e+02 angle pdb=" C5 ATP B 801 " pdb=" C4 ATP B 801 " pdb=" N3 ATP B 801 " ideal model delta sigma weight residual 126.80 117.87 8.93 1.00e+00 1.00e+00 7.98e+01 ... (remaining 12902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5009 17.73 - 35.46: 528 35.46 - 53.19: 93 53.19 - 70.91: 9 70.91 - 88.64: 10 Dihedral angle restraints: 5649 sinusoidal: 2286 harmonic: 3363 Sorted by residual: dihedral pdb=" CA LYS A 533 " pdb=" C LYS A 533 " pdb=" N PRO A 534 " pdb=" CA PRO A 534 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LYS B 533 " pdb=" C LYS B 533 " pdb=" N PRO B 534 " pdb=" CA PRO B 534 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA SER A 572 " pdb=" C SER A 572 " pdb=" N GLU A 573 " pdb=" CA GLU A 573 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1207 0.054 - 0.107: 193 0.107 - 0.161: 31 0.161 - 0.214: 2 0.214 - 0.268: 2 Chirality restraints: 1435 Sorted by residual: chirality pdb=" C2' ATP A 801 " pdb=" C1' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O2' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C2' ATP B 801 " pdb=" C1' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" O2' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3' ATP B 801 " pdb=" C2' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" O3' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1432 not shown) Planarity restraints: 1625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 479 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 480 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 507 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO B 508 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 508 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 508 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 507 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 508 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " -0.023 5.00e-02 4.00e+02 ... (remaining 1622 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 243 2.71 - 3.26: 9472 3.26 - 3.81: 14957 3.81 - 4.35: 18728 4.35 - 4.90: 32503 Nonbonded interactions: 75903 Sorted by model distance: nonbonded pdb=" OG1 THR B 506 " pdb=" OE1 GLN B 672 " model vdw 2.163 2.440 nonbonded pdb=" O PRO B 508 " pdb=" NZ LYS B 513 " model vdw 2.253 2.520 nonbonded pdb=" O TYR B 547 " pdb=" NH2 ARG B 617 " model vdw 2.290 2.520 nonbonded pdb=" O GLN B 472 " pdb=" OH TYR B 625 " model vdw 2.294 2.440 nonbonded pdb=" O TYR A 547 " pdb=" NH2 ARG A 617 " model vdw 2.295 2.520 ... (remaining 75898 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' and (resid 64 through 353 or resid 371 through 682 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.200 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: 0.010 Extract box with map and model: 13.210 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 28.560 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.225 9523 Z= 0.428 Angle : 0.764 14.464 12907 Z= 0.506 Chirality : 0.042 0.268 1435 Planarity : 0.004 0.045 1625 Dihedral : 14.720 88.644 3487 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1147 helix: 0.80 (0.20), residues: 746 sheet: -2.70 (0.84), residues: 32 loop : -3.15 (0.28), residues: 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.085 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2997 time to fit residues: 44.7867 Evaluate side-chains 86 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 289 ASN A 420 HIS A 433 HIS ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9523 Z= 0.265 Angle : 0.587 8.380 12907 Z= 0.299 Chirality : 0.040 0.149 1435 Planarity : 0.004 0.043 1625 Dihedral : 5.316 56.789 1299 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.72 % Allowed : 6.88 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1147 helix: 0.85 (0.19), residues: 755 sheet: -2.89 (0.76), residues: 36 loop : -3.18 (0.29), residues: 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.075 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.2444 time to fit residues: 31.4776 Evaluate side-chains 87 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0965 time to fit residues: 2.3915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 0.0060 chunk 103 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9523 Z= 0.190 Angle : 0.529 7.418 12907 Z= 0.271 Chirality : 0.038 0.148 1435 Planarity : 0.004 0.042 1625 Dihedral : 5.038 55.978 1299 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.82 % Allowed : 9.65 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1147 helix: 1.08 (0.19), residues: 755 sheet: -2.55 (0.83), residues: 34 loop : -3.02 (0.29), residues: 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.055 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 101 average time/residue: 0.2114 time to fit residues: 31.0407 Evaluate side-chains 87 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0836 time to fit residues: 1.9967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 49 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9523 Z= 0.288 Angle : 0.571 6.925 12907 Z= 0.291 Chirality : 0.040 0.153 1435 Planarity : 0.004 0.044 1625 Dihedral : 5.100 52.994 1299 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.16 % Allowed : 12.83 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1147 helix: 0.97 (0.19), residues: 753 sheet: -2.91 (0.76), residues: 36 loop : -3.02 (0.29), residues: 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.086 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 105 average time/residue: 0.2501 time to fit residues: 36.0855 Evaluate side-chains 91 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0869 time to fit residues: 2.7985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 37 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9523 Z= 0.219 Angle : 0.542 10.373 12907 Z= 0.275 Chirality : 0.039 0.250 1435 Planarity : 0.004 0.040 1625 Dihedral : 4.876 48.434 1299 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.03 % Allowed : 14.07 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1147 helix: 1.16 (0.19), residues: 753 sheet: -2.79 (0.79), residues: 36 loop : -2.97 (0.29), residues: 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.135 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 97 average time/residue: 0.2317 time to fit residues: 31.9945 Evaluate side-chains 88 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1023 time to fit residues: 2.4164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7885 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9523 Z= 0.278 Angle : 0.565 9.666 12907 Z= 0.286 Chirality : 0.041 0.241 1435 Planarity : 0.004 0.041 1625 Dihedral : 4.952 47.381 1299 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.13 % Allowed : 14.99 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1147 helix: 1.09 (0.19), residues: 753 sheet: -2.81 (0.79), residues: 36 loop : -2.92 (0.29), residues: 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.048 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 93 average time/residue: 0.2363 time to fit residues: 30.9982 Evaluate side-chains 87 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0928 time to fit residues: 2.5337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 0.0980 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 67 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7838 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9523 Z= 0.197 Angle : 0.526 8.599 12907 Z= 0.266 Chirality : 0.039 0.231 1435 Planarity : 0.004 0.040 1625 Dihedral : 4.686 44.327 1299 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.82 % Allowed : 15.09 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1147 helix: 1.30 (0.19), residues: 754 sheet: -2.56 (0.85), residues: 35 loop : -2.86 (0.30), residues: 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.024 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 0.2357 time to fit residues: 31.1194 Evaluate side-chains 82 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0889 time to fit residues: 2.1018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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: 0.7845 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9523 Z= 0.218 Angle : 0.537 8.153 12907 Z= 0.270 Chirality : 0.039 0.218 1435 Planarity : 0.004 0.040 1625 Dihedral : 4.640 42.600 1299 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.62 % Allowed : 15.61 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1147 helix: 1.31 (0.19), residues: 753 sheet: -2.51 (0.85), residues: 35 loop : -2.86 (0.30), residues: 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.029 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 0.2313 time to fit residues: 28.8254 Evaluate side-chains 83 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1069 time to fit residues: 2.2129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 62 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 0.0000 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9523 Z= 0.168 Angle : 0.515 7.515 12907 Z= 0.259 Chirality : 0.038 0.208 1435 Planarity : 0.004 0.040 1625 Dihedral : 4.407 38.413 1299 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1147 helix: 1.49 (0.19), residues: 751 sheet: -2.28 (0.95), residues: 33 loop : -2.76 (0.30), residues: 363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.058 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2340 time to fit residues: 31.9601 Evaluate side-chains 82 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 97 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9523 Z= 0.191 Angle : 0.526 7.387 12907 Z= 0.265 Chirality : 0.039 0.202 1435 Planarity : 0.004 0.043 1625 Dihedral : 4.384 36.850 1299 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 16.84 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1147 helix: 1.50 (0.19), residues: 750 sheet: -2.25 (0.95), residues: 33 loop : -2.74 (0.30), residues: 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.023 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2304 time to fit residues: 27.2802 Evaluate side-chains 80 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.3980 chunk 84 optimal weight: 0.0000 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 93 optimal weight: 0.0470 chunk 11 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 HIS ** 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 = 0.3917 r_free = 0.3917 target = 0.176239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132804 restraints weight = 9080.608| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.71 r_work: 0.3350 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9523 Z= 0.146 Angle : 0.503 6.903 12907 Z= 0.253 Chirality : 0.038 0.201 1435 Planarity : 0.004 0.042 1625 Dihedral : 4.134 31.698 1299 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.10 % Allowed : 16.94 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1147 helix: 1.60 (0.19), residues: 757 sheet: -2.11 (0.97), residues: 33 loop : -2.64 (0.31), residues: 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.48 seconds wall clock time: 40 minutes 53.73 seconds (2453.73 seconds total)