Starting phenix.real_space_refine on Thu Nov 16 19:19:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/11_2023/7vd9_31911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/11_2023/7vd9_31911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/11_2023/7vd9_31911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/11_2023/7vd9_31911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/11_2023/7vd9_31911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/11_2023/7vd9_31911_updated.pdb" } resolution = 2.29 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= 0.006 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10421 2.51 5 N 2895 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "B" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "C" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "D" Number of atoms: 4011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Conformer: "B" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} bond proxies already assigned to first conformer: 4109 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ASER A 120 " occ=0.63 ... (10 atoms not shown) pdb=" OG BSER A 120 " occ=0.37 residue: pdb=" N AGLY A 121 " occ=0.63 ... (6 atoms not shown) pdb=" O BGLY A 121 " occ=0.37 residue: pdb=" N ASER B 120 " occ=0.82 ... (10 atoms not shown) pdb=" OG BSER B 120 " occ=0.18 residue: pdb=" N AGLY B 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY B 121 " occ=0.18 residue: pdb=" N ASER C 120 " occ=0.64 ... (10 atoms not shown) pdb=" OG BSER C 120 " occ=0.36 residue: pdb=" N AGLY C 121 " occ=0.64 ... (6 atoms not shown) pdb=" O BGLY C 121 " occ=0.36 residue: pdb=" N ASER D 120 " occ=0.89 ... (10 atoms not shown) pdb=" OG BSER D 120 " occ=0.11 residue: pdb=" N AGLY D 121 " occ=0.89 ... (6 atoms not shown) pdb=" O BGLY D 121 " occ=0.11 Time building chain proxies: 15.59, per 1000 atoms: 0.95 Number of scatterers: 16426 At special positions: 0 Unit cell: (113.1, 109.2, 83.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3042 8.00 N 2895 7.00 C 10421 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: 7.54 Conformation dependent library (CDL) restraints added in 6.3 seconds 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 4 sheets defined 34.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 6.744A pdb=" N MET A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLN A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 158 through 168 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 190 through 200 removed outlier: 4.168A pdb=" N HIS A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 325 through 328 No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 349 through 366 removed outlier: 3.728A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 441 through 449 Processing helix chain 'A' and resid 453 through 469 removed outlier: 5.047A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 487 through 500 Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 158 through 168 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.138A pdb=" N HIS B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 325 through 328 No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 349 through 366 removed outlier: 3.755A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 453 through 469 removed outlier: 4.989A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 55 through 66 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 158 through 168 Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 179 through 188 Processing helix chain 'C' and resid 190 through 200 removed outlier: 4.179A pdb=" N HIS C 194 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 325 through 328 No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 349 through 365 removed outlier: 3.709A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 441 through 449 Processing helix chain 'C' and resid 453 through 469 removed outlier: 5.006A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 487 through 500 Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.620A pdb=" N ARG D 19 " --> pdb=" O TRP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 158 through 168 Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 190 through 199 removed outlier: 4.059A pdb=" N HIS D 194 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 325 through 328 No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 349 through 365 removed outlier: 3.717A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Proline residue: D 359 - end of helix Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 441 through 448 Processing helix chain 'D' and resid 453 through 467 Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 487 through 500 Processing sheet with id= A, first strand: chain 'A' and resid 141 through 148 removed outlier: 7.108A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 141 through 148 removed outlier: 7.117A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE B 279 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS B 315 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP B 277 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 141 through 148 removed outlier: 7.123A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 141 through 148 removed outlier: 7.095A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1389 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: 4.58 Time building geometry restraints manager: 8.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 7276 1.39 - 1.56: 9542 1.56 - 1.73: 20 1.73 - 1.89: 96 1.89 - 2.06: 16 Bond restraints: 16950 Sorted by residual: bond pdb=" CG PRO D 406 " pdb=" CD PRO D 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.91e-01 bond pdb=" CG PRO C 406 " pdb=" CD PRO C 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.84e-01 bond pdb=" CG PRO B 406 " pdb=" CD PRO B 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.69e-01 bond pdb=" CB GLU D 290 " pdb=" CG GLU D 290 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.57e-01 bond pdb=" CB GLN B 195 " pdb=" CG GLN B 195 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.06e-01 ... (remaining 16945 not shown) Histogram of bond angle deviations from ideal: 89.04 - 107.10: 817 107.10 - 125.15: 21806 125.15 - 143.21: 497 143.21 - 161.26: 0 161.26 - 179.31: 8 Bond angle restraints: 23128 Sorted by residual: angle pdb=" C ARG D 388 " pdb=" N ASP D 389 " pdb=" CA ASP D 389 " ideal model delta sigma weight residual 121.31 126.88 -5.57 1.49e+00 4.50e-01 1.40e+01 angle pdb=" C ARG B 388 " pdb=" N ASP B 389 " pdb=" CA ASP B 389 " ideal model delta sigma weight residual 121.31 126.77 -5.46 1.49e+00 4.50e-01 1.34e+01 angle pdb=" CB MET D 394 " pdb=" CG MET D 394 " pdb=" SD MET D 394 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C ARG A 388 " pdb=" N ASP A 389 " pdb=" CA ASP A 389 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.74e+00 angle pdb=" N ASP D 389 " pdb=" CA ASP D 389 " pdb=" C ASP D 389 " ideal model delta sigma weight residual 110.35 114.40 -4.05 1.40e+00 5.10e-01 8.39e+00 ... (remaining 23123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8631 17.69 - 35.38: 876 35.38 - 53.07: 273 53.07 - 70.76: 80 70.76 - 88.45: 36 Dihedral angle restraints: 9896 sinusoidal: 4087 harmonic: 5809 Sorted by residual: dihedral pdb=" CA CYS D 393 " pdb=" C CYS D 393 " pdb=" N MET D 394 " pdb=" CA MET D 394 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASP D 180 " pdb=" CB ASP D 180 " pdb=" CG ASP D 180 " pdb=" OD1 ASP D 180 " ideal model delta sinusoidal sigma weight residual -30.00 -88.06 58.06 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 180 " pdb=" CB ASP A 180 " pdb=" CG ASP A 180 " pdb=" OD1 ASP A 180 " ideal model delta sinusoidal sigma weight residual -30.00 -87.20 57.20 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 9893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1331 0.029 - 0.059: 650 0.059 - 0.088: 208 0.088 - 0.118: 127 0.118 - 0.147: 19 Chirality restraints: 2335 Sorted by residual: chirality pdb=" CA ILE B 373 " pdb=" N ILE B 373 " pdb=" C ILE B 373 " pdb=" CB ILE B 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE C 373 " pdb=" N ILE C 373 " pdb=" C ILE C 373 " pdb=" CB ILE C 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA TYR C 358 " pdb=" N TYR C 358 " pdb=" C TYR C 358 " pdb=" CB TYR C 358 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2332 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 6 " -0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO C 7 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 346 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO C 347 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 346 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 347 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 347 " -0.026 5.00e-02 4.00e+02 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1009 2.74 - 3.28: 16266 3.28 - 3.82: 29828 3.82 - 4.36: 36824 4.36 - 4.90: 60764 Nonbonded interactions: 144691 Sorted by model distance: nonbonded pdb=" NE2 GLN A 415 " pdb=" OG SER A 417 " model vdw 2.194 2.520 nonbonded pdb=" OE1 GLN D 415 " pdb=" OG SER D 417 " model vdw 2.224 2.440 nonbonded pdb=" NZ LYS B 301 " pdb=" O ASP B 438 " model vdw 2.226 2.520 nonbonded pdb=" OD2 ASP A 360 " pdb=" NH1 ARG C 66 " model vdw 2.231 2.520 nonbonded pdb=" NZ LYS D 301 " pdb=" O ASP D 438 " model vdw 2.232 2.520 ... (remaining 144686 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' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 5 through 119 or resid 122 through 501 or resid 1201 throu \ gh 1202)) selection = (chain 'C' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) selection = (chain 'D' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) } 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=0.11 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: 2.750 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: 8.220 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 57.490 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.150 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:16.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 : 0.002 0.044 16950 Z= 0.158 Angle : 0.543 10.399 23128 Z= 0.272 Chirality : 0.042 0.147 2335 Planarity : 0.005 0.063 3067 Dihedral : 17.252 88.450 6170 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.33 % Allowed : 18.62 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.41 (0.19), residues: 1999 helix: 1.21 (0.20), residues: 698 sheet: 0.61 (0.33), residues: 283 loop : -0.45 (0.20), residues: 1018 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 2.126 Fit side-chains outliers start: 38 outliers final: 35 residues processed: 231 average time/residue: 1.2361 time to fit residues: 320.9894 Evaluate side-chains 213 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 1.816 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 34 residues processed: 2 average time/residue: 0.2099 time to fit residues: 3.1415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 100 optimal weight: 0.1980 chunk 79 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 177 optimal weight: 0.0670 overall best weight: 3.2524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16950 Z= 0.268 Angle : 0.667 6.564 23128 Z= 0.346 Chirality : 0.047 0.167 2335 Planarity : 0.006 0.061 3067 Dihedral : 8.449 92.081 2267 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.36 % Allowed : 17.51 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 1999 helix: 0.37 (0.19), residues: 699 sheet: 0.40 (0.31), residues: 296 loop : -0.58 (0.19), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 174 time to evaluate : 2.230 Fit side-chains outliers start: 73 outliers final: 47 residues processed: 232 average time/residue: 1.1787 time to fit residues: 309.5839 Evaluate side-chains 218 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 171 time to evaluate : 1.698 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 42 residues processed: 5 average time/residue: 0.4203 time to fit residues: 5.1378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16950 Z= 0.360 Angle : 0.765 8.295 23128 Z= 0.400 Chirality : 0.051 0.179 2335 Planarity : 0.007 0.061 3067 Dihedral : 8.831 93.026 2267 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.71 % Allowed : 16.93 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.72 (0.18), residues: 1999 helix: -0.33 (0.19), residues: 699 sheet: 0.34 (0.31), residues: 296 loop : -0.76 (0.19), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 182 time to evaluate : 1.861 Fit side-chains outliers start: 79 outliers final: 52 residues processed: 250 average time/residue: 1.1842 time to fit residues: 334.7239 Evaluate side-chains 227 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 175 time to evaluate : 1.900 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 48 residues processed: 4 average time/residue: 0.1723 time to fit residues: 3.9730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 overall best weight: 3.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 40 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 ASN D 492 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16950 Z= 0.279 Angle : 0.679 6.856 23128 Z= 0.354 Chirality : 0.048 0.146 2335 Planarity : 0.006 0.060 3067 Dihedral : 8.270 85.694 2267 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.71 % Allowed : 17.22 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.68 (0.18), residues: 1999 helix: -0.24 (0.19), residues: 699 sheet: 0.31 (0.31), residues: 300 loop : -0.77 (0.19), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 172 time to evaluate : 2.104 Fit side-chains outliers start: 79 outliers final: 59 residues processed: 239 average time/residue: 1.1865 time to fit residues: 321.0268 Evaluate side-chains 229 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 170 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 52 residues processed: 7 average time/residue: 0.3511 time to fit residues: 5.7969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 0.0670 chunk 78 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 170 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 overall best weight: 3.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 494 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16950 Z= 0.266 Angle : 0.666 6.674 23128 Z= 0.347 Chirality : 0.047 0.147 2335 Planarity : 0.006 0.059 3067 Dihedral : 8.189 84.418 2267 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.65 % Allowed : 16.99 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.66 (0.18), residues: 1999 helix: -0.22 (0.19), residues: 699 sheet: 0.31 (0.31), residues: 300 loop : -0.75 (0.19), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 177 time to evaluate : 1.851 Fit side-chains outliers start: 78 outliers final: 56 residues processed: 247 average time/residue: 1.1721 time to fit residues: 327.0038 Evaluate side-chains 229 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 173 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 53 residues processed: 3 average time/residue: 0.1810 time to fit residues: 3.5407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 494 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16950 Z= 0.344 Angle : 0.749 8.107 23128 Z= 0.392 Chirality : 0.050 0.146 2335 Planarity : 0.007 0.059 3067 Dihedral : 8.681 87.387 2267 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.83 % Allowed : 16.99 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.91 (0.18), residues: 1999 helix: -0.48 (0.18), residues: 698 sheet: 0.25 (0.30), residues: 300 loop : -0.88 (0.19), residues: 1001 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 179 time to evaluate : 1.707 Fit side-chains outliers start: 81 outliers final: 64 residues processed: 247 average time/residue: 1.1535 time to fit residues: 321.3232 Evaluate side-chains 238 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 174 time to evaluate : 1.822 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 56 residues processed: 8 average time/residue: 0.5034 time to fit residues: 7.6343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 40 ASN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16950 Z= 0.200 Angle : 0.593 6.239 23128 Z= 0.307 Chirality : 0.045 0.147 2335 Planarity : 0.005 0.059 3067 Dihedral : 7.418 74.555 2267 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.84 % Allowed : 18.15 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.47 (0.18), residues: 1999 helix: -0.02 (0.19), residues: 699 sheet: 0.39 (0.31), residues: 300 loop : -0.66 (0.19), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 190 time to evaluate : 2.040 Fit side-chains outliers start: 64 outliers final: 52 residues processed: 246 average time/residue: 1.1490 time to fit residues: 321.0943 Evaluate side-chains 222 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 170 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 47 residues processed: 5 average time/residue: 0.7464 time to fit residues: 6.9280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 148 optimal weight: 0.0060 overall best weight: 0.9918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 53 GLN ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS C 492 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16950 Z= 0.164 Angle : 0.547 6.898 23128 Z= 0.278 Chirality : 0.044 0.148 2335 Planarity : 0.005 0.057 3067 Dihedral : 6.593 62.198 2267 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.32 % Allowed : 18.79 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.14 (0.19), residues: 1999 helix: 0.30 (0.19), residues: 699 sheet: 0.60 (0.31), residues: 297 loop : -0.51 (0.19), residues: 1003 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 1.863 Fit side-chains outliers start: 55 outliers final: 40 residues processed: 241 average time/residue: 1.1583 time to fit residues: 315.9048 Evaluate side-chains 217 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 40 residues processed: 0 time to fit residues: 2.6185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 53 GLN ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 492 HIS B 494 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS C 492 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16950 Z= 0.162 Angle : 0.545 7.171 23128 Z= 0.275 Chirality : 0.043 0.149 2335 Planarity : 0.005 0.056 3067 Dihedral : 6.499 63.605 2267 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.56 % Allowed : 19.55 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.00 (0.19), residues: 1999 helix: 0.44 (0.19), residues: 700 sheet: 0.67 (0.31), residues: 296 loop : -0.45 (0.19), residues: 1003 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 2.063 Fit side-chains outliers start: 42 outliers final: 39 residues processed: 225 average time/residue: 1.2599 time to fit residues: 320.4985 Evaluate side-chains 215 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 39 residues processed: 0 time to fit residues: 2.5968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 88 optimal weight: 0.0170 chunk 129 optimal weight: 10.0000 chunk 195 optimal weight: 0.0980 chunk 179 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 overall best weight: 3.0224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16950 Z= 0.256 Angle : 0.655 6.761 23128 Z= 0.337 Chirality : 0.047 0.146 2335 Planarity : 0.006 0.057 3067 Dihedral : 7.827 75.425 2267 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.85 % Allowed : 19.20 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.18), residues: 1999 helix: 0.15 (0.19), residues: 699 sheet: 0.59 (0.31), residues: 296 loop : -0.60 (0.19), residues: 1004 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 179 time to evaluate : 1.903 Fit side-chains outliers start: 47 outliers final: 39 residues processed: 223 average time/residue: 1.2627 time to fit residues: 316.4341 Evaluate side-chains 216 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 39 residues processed: 0 time to fit residues: 2.5638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 494 GLN ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.169558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143918 restraints weight = 25645.623| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.50 r_work: 0.3541 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.002 0.038 16950 Z= 0.158 Angle : 0.544 7.233 23128 Z= 0.275 Chirality : 0.043 0.146 2335 Planarity : 0.005 0.056 3067 Dihedral : 6.329 58.728 2267 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.56 % Allowed : 19.43 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.00 (0.19), residues: 1999 helix: 0.48 (0.20), residues: 700 sheet: 0.60 (0.30), residues: 297 loop : -0.45 (0.20), residues: 1002 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5909.04 seconds wall clock time: 106 minutes 3.17 seconds (6363.17 seconds total)