Starting phenix.real_space_refine on Wed Mar 4 05:39:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zqs_14874/03_2026/7zqs_14874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zqs_14874/03_2026/7zqs_14874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zqs_14874/03_2026/7zqs_14874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zqs_14874/03_2026/7zqs_14874.map" model { file = "/net/cci-nas-00/data/ceres_data/7zqs_14874/03_2026/7zqs_14874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zqs_14874/03_2026/7zqs_14874.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 sd= 0.023 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 P 60 5.49 5 Mg 4 5.21 5 S 28 5.16 5 C 7068 2.51 5 N 1936 2.21 5 O 2258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11354 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 634 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "B" Number of atoms: 4971 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 639, 4964 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 75 Conformer: "B" Number of residues, atoms: 639, 4964 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 75 bond proxies already assigned to first conformer: 5075 Chain: "C" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 634 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 4971 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 639, 4964 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 75 Conformer: "B" Number of residues, atoms: 639, 4964 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 75 bond proxies already assigned to first conformer: 5075 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.56, per 1000 atoms: 0.40 Number of scatterers: 11354 At special positions: 0 Unit cell: (129.514, 107.505, 93.9615, 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) S 28 16.00 P 60 15.00 Mg 4 11.99 O 2258 8.00 N 1936 7.00 C 7068 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 - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 801 " - " ASN B 251 " " NAG D 801 " - " ASN D 251 " " NAG E 1 " - " ASN B 317 " " NAG F 1 " - " ASN B 727 " " NAG G 1 " - " ASN D 317 " " NAG H 1 " - " ASN D 727 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 697.7 milliseconds 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 45.1% alpha, 16.9% beta 8 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.716A pdb=" N SER B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'B' and resid 159 through 176 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.609A pdb=" N LEU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 419 through 439 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 470 through 475 Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.665A pdb=" N VAL B 532 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.173A pdb=" N PHE B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 582 through 603 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 613 through 626 removed outlier: 3.741A pdb=" N GLN B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 663 Processing helix chain 'B' and resid 667 through 684 removed outlier: 3.765A pdb=" N VAL B 681 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU B 682 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR B 683 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 Processing helix chain 'B' and resid 727 through 751 removed outlier: 3.677A pdb=" N GLY B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.630A pdb=" N ILE B 756 " --> pdb=" O VAL B 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 137 removed outlier: 3.716A pdb=" N SER D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 148 Processing helix chain 'D' and resid 159 through 176 Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 263 through 274 removed outlier: 3.609A pdb=" N LEU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 419 through 439 Processing helix chain 'D' and resid 455 through 459 Processing helix chain 'D' and resid 460 through 470 Processing helix chain 'D' and resid 470 through 475 Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 527 through 532 removed outlier: 3.664A pdb=" N VAL D 532 " --> pdb=" O ALA D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.174A pdb=" N PHE D 544 " --> pdb=" O ALA D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 582 through 603 Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 613 through 626 removed outlier: 3.741A pdb=" N GLN D 617 " --> pdb=" O ARG D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 639 through 663 Processing helix chain 'D' and resid 667 through 684 removed outlier: 3.764A pdb=" N VAL D 681 " --> pdb=" O ARG D 677 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU D 682 " --> pdb=" O VAL D 678 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR D 683 " --> pdb=" O MET D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 722 Processing helix chain 'D' and resid 727 through 751 removed outlier: 3.676A pdb=" N GLY D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 756 removed outlier: 3.630A pdb=" N ILE D 756 " --> pdb=" O VAL D 753 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 180 through 182 removed outlier: 7.150A pdb=" N TYR B 402 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE B 482 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 404 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 180 through 182 removed outlier: 7.150A pdb=" N TYR B 402 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE B 482 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 404 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 185 through 192 Processing sheet with id=AA4, first strand: chain 'B' and resid 209 through 214 removed outlier: 5.615A pdb=" N LEU B 212 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 202 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AA7, first strand: chain 'D' and resid 180 through 182 removed outlier: 7.150A pdb=" N TYR D 402 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE D 482 " --> pdb=" O TYR D 402 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 404 " --> pdb=" O ILE D 482 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE D 555 " --> pdb=" O ASN D 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 180 through 182 removed outlier: 7.150A pdb=" N TYR D 402 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE D 482 " --> pdb=" O TYR D 402 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 404 " --> pdb=" O ILE D 482 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE D 555 " --> pdb=" O ASN D 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 185 through 192 Processing sheet with id=AB1, first strand: chain 'D' and resid 209 through 214 removed outlier: 5.613A pdb=" N LEU D 212 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE D 202 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AB3, first strand: chain 'D' and resid 232 through 234 518 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2618 1.33 - 1.45: 2783 1.45 - 1.57: 6181 1.57 - 1.69: 118 1.69 - 1.80: 48 Bond restraints: 11748 Sorted by residual: bond pdb=" C3' DA C 12 " pdb=" O3' DA C 12 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.54e+00 bond pdb=" C3' DA A 12 " pdb=" O3' DA A 12 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" C1 NAG B 801 " pdb=" O5 NAG B 801 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG D 801 " pdb=" O5 NAG D 801 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 11743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 15632 1.31 - 2.62: 485 2.62 - 3.93: 86 3.93 - 5.24: 23 5.24 - 6.55: 6 Bond angle restraints: 16232 Sorted by residual: angle pdb=" N VAL B 250 " pdb=" CA VAL B 250 " pdb=" C VAL B 250 " ideal model delta sigma weight residual 106.21 110.71 -4.50 1.07e+00 8.73e-01 1.77e+01 angle pdb=" N VAL D 250 " pdb=" CA VAL D 250 " pdb=" C VAL D 250 " ideal model delta sigma weight residual 106.21 110.68 -4.47 1.07e+00 8.73e-01 1.74e+01 angle pdb=" N VAL B 210 " pdb=" CA VAL B 210 " pdb=" C VAL B 210 " ideal model delta sigma weight residual 111.48 108.24 3.24 9.40e-01 1.13e+00 1.19e+01 angle pdb=" N VAL D 210 " pdb=" CA VAL D 210 " pdb=" C VAL D 210 " ideal model delta sigma weight residual 111.48 108.25 3.23 9.40e-01 1.13e+00 1.18e+01 angle pdb=" CA TRP B 740 " pdb=" CB TRP B 740 " pdb=" CG TRP B 740 " ideal model delta sigma weight residual 113.60 107.67 5.93 1.90e+00 2.77e-01 9.75e+00 ... (remaining 16227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 6500 34.25 - 68.51: 326 68.51 - 102.76: 16 102.76 - 137.01: 0 137.01 - 171.26: 4 Dihedral angle restraints: 6846 sinusoidal: 3128 harmonic: 3718 Sorted by residual: dihedral pdb=" CA PHE B 313 " pdb=" C PHE B 313 " pdb=" N PRO B 314 " pdb=" CA PRO B 314 " ideal model delta harmonic sigma weight residual -180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE D 313 " pdb=" C PHE D 313 " pdb=" N PRO D 314 " pdb=" CA PRO D 314 " ideal model delta harmonic sigma weight residual 180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C4' DG A 31 " pdb=" C3' DG A 31 " pdb=" O3' DG A 31 " pdb=" P DT A 32 " ideal model delta sinusoidal sigma weight residual 220.00 48.74 171.26 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1560 0.054 - 0.109: 239 0.109 - 0.163: 35 0.163 - 0.218: 4 0.218 - 0.272: 2 Chirality restraints: 1840 Sorted by residual: chirality pdb=" CB ILE D 262 " pdb=" CA ILE D 262 " pdb=" CG1 ILE D 262 " pdb=" CG2 ILE D 262 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE B 262 " pdb=" CA ILE B 262 " pdb=" CG1 ILE B 262 " pdb=" CG2 ILE B 262 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 727 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 1837 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 261 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LYS D 261 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS D 261 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE D 262 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 261 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C LYS B 261 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS B 261 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 262 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 740 " -0.016 2.00e-02 2.50e+03 1.02e-02 2.60e+00 pdb=" CG TRP D 740 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP D 740 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 740 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 740 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 740 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 740 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 740 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 740 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 740 " -0.003 2.00e-02 2.50e+03 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2608 2.79 - 3.31: 10660 3.31 - 3.84: 20892 3.84 - 4.37: 25782 4.37 - 4.90: 41451 Nonbonded interactions: 101393 Sorted by model distance: nonbonded pdb=" OP2 DG A 34 " pdb="MG MG A 101 " model vdw 2.257 2.170 nonbonded pdb=" OP2 DG C 34 " pdb="MG MG C 101 " model vdw 2.259 2.170 nonbonded pdb=" O LEU B 387 " pdb=" NH2 ARG B 409 " model vdw 2.267 3.120 nonbonded pdb=" O LEU D 387 " pdb=" NH2 ARG D 409 " model vdw 2.268 3.120 nonbonded pdb=" OP2 DA C 35 " pdb="MG MG C 101 " model vdw 2.269 2.170 ... (remaining 101388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 120 through 639 or resid 641 through 801)) selection = (chain 'D' and (resid 120 through 639 or resid 641 through 801)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.50 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.170 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:8.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 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 : 0.004 0.048 11758 Z= 0.190 Angle : 0.572 6.547 16262 Z= 0.326 Chirality : 0.042 0.272 1840 Planarity : 0.003 0.031 1842 Dihedral : 17.997 171.262 4454 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1278 helix: 1.49 (0.22), residues: 544 sheet: 0.94 (0.34), residues: 202 loop : 0.33 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 623 TYR 0.013 0.001 TYR D 309 PHE 0.019 0.002 PHE D 313 TRP 0.027 0.002 TRP D 740 HIS 0.004 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00421 (11748) covalent geometry : angle 0.56841 (16232) hydrogen bonds : bond 0.15010 ( 498) hydrogen bonds : angle 5.85480 ( 1464) link_BETA1-4 : bond 0.00265 ( 4) link_BETA1-4 : angle 2.02082 ( 12) link_NAG-ASN : bond 0.00157 ( 6) link_NAG-ASN : angle 1.33549 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.385 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.8494 time to fit residues: 25.6871 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.053658 restraints weight = 43051.013| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.68 r_work: 0.2743 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11758 Z= 0.149 Angle : 0.541 7.816 16262 Z= 0.298 Chirality : 0.043 0.291 1840 Planarity : 0.004 0.029 1842 Dihedral : 19.818 172.170 2210 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.24), residues: 1278 helix: 1.72 (0.23), residues: 540 sheet: 1.12 (0.35), residues: 202 loop : 0.48 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 668 TYR 0.010 0.001 TYR D 309 PHE 0.019 0.002 PHE D 313 TRP 0.024 0.002 TRP B 740 HIS 0.003 0.001 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00337 (11748) covalent geometry : angle 0.53874 (16232) hydrogen bonds : bond 0.04876 ( 498) hydrogen bonds : angle 4.20272 ( 1464) link_BETA1-4 : bond 0.00245 ( 4) link_BETA1-4 : angle 1.38693 ( 12) link_NAG-ASN : bond 0.00219 ( 6) link_NAG-ASN : angle 1.36051 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.410 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.7482 time to fit residues: 17.3134 Evaluate side-chains 21 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 76 optimal weight: 5.9990 chunk 35 optimal weight: 0.0070 chunk 63 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054959 restraints weight = 42948.650| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.67 r_work: 0.2782 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11758 Z= 0.120 Angle : 0.490 6.347 16262 Z= 0.270 Chirality : 0.041 0.274 1840 Planarity : 0.003 0.028 1842 Dihedral : 19.552 171.102 2210 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.25), residues: 1278 helix: 1.92 (0.23), residues: 542 sheet: 1.26 (0.35), residues: 202 loop : 0.61 (0.30), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 623 TYR 0.010 0.001 TYR B 309 PHE 0.019 0.001 PHE B 313 TRP 0.022 0.002 TRP D 740 HIS 0.003 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00267 (11748) covalent geometry : angle 0.48766 (16232) hydrogen bonds : bond 0.04200 ( 498) hydrogen bonds : angle 3.88369 ( 1464) link_BETA1-4 : bond 0.00268 ( 4) link_BETA1-4 : angle 1.32155 ( 12) link_NAG-ASN : bond 0.00153 ( 6) link_NAG-ASN : angle 1.26445 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.419 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.7568 time to fit residues: 17.5327 Evaluate side-chains 21 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.070478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.052872 restraints weight = 42706.478| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.66 r_work: 0.2728 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11758 Z= 0.196 Angle : 0.533 6.354 16262 Z= 0.291 Chirality : 0.043 0.218 1840 Planarity : 0.003 0.036 1842 Dihedral : 19.656 171.131 2210 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1278 helix: 1.84 (0.22), residues: 540 sheet: 1.15 (0.37), residues: 186 loop : 0.59 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.012 0.001 TYR B 470 PHE 0.017 0.002 PHE D 313 TRP 0.023 0.002 TRP D 740 HIS 0.004 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00457 (11748) covalent geometry : angle 0.53051 (16232) hydrogen bonds : bond 0.04374 ( 498) hydrogen bonds : angle 3.94812 ( 1464) link_BETA1-4 : bond 0.00141 ( 4) link_BETA1-4 : angle 1.46093 ( 12) link_NAG-ASN : bond 0.00096 ( 6) link_NAG-ASN : angle 1.31101 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.421 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.7238 time to fit residues: 17.6130 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.054852 restraints weight = 42447.470| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.66 r_work: 0.2807 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11758 Z= 0.122 Angle : 0.486 6.100 16262 Z= 0.268 Chirality : 0.041 0.223 1840 Planarity : 0.003 0.032 1842 Dihedral : 19.555 170.654 2210 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.25), residues: 1278 helix: 1.98 (0.23), residues: 540 sheet: 1.23 (0.37), residues: 186 loop : 0.65 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 668 TYR 0.010 0.001 TYR D 309 PHE 0.018 0.001 PHE D 313 TRP 0.021 0.002 TRP D 740 HIS 0.002 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00275 (11748) covalent geometry : angle 0.48367 (16232) hydrogen bonds : bond 0.03908 ( 498) hydrogen bonds : angle 3.78112 ( 1464) link_BETA1-4 : bond 0.00275 ( 4) link_BETA1-4 : angle 1.32060 ( 12) link_NAG-ASN : bond 0.00188 ( 6) link_NAG-ASN : angle 1.30580 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.306 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.7176 time to fit residues: 17.5043 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.070738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.052777 restraints weight = 53924.149| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.95 r_work: 0.2714 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11758 Z= 0.193 Angle : 0.522 5.844 16262 Z= 0.286 Chirality : 0.042 0.188 1840 Planarity : 0.003 0.038 1842 Dihedral : 19.609 170.700 2210 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.24), residues: 1278 helix: 1.88 (0.22), residues: 540 sheet: 1.13 (0.37), residues: 186 loop : 0.61 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.012 0.001 TYR B 470 PHE 0.020 0.002 PHE D 731 TRP 0.022 0.002 TRP D 740 HIS 0.003 0.001 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00450 (11748) covalent geometry : angle 0.51916 (16232) hydrogen bonds : bond 0.04215 ( 498) hydrogen bonds : angle 3.86108 ( 1464) link_BETA1-4 : bond 0.00192 ( 4) link_BETA1-4 : angle 1.47278 ( 12) link_NAG-ASN : bond 0.00097 ( 6) link_NAG-ASN : angle 1.32639 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.421 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.6703 time to fit residues: 17.7880 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 90 optimal weight: 0.0170 chunk 116 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053504 restraints weight = 42792.719| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.67 r_work: 0.2743 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11758 Z= 0.148 Angle : 0.509 5.959 16262 Z= 0.279 Chirality : 0.041 0.199 1840 Planarity : 0.003 0.037 1842 Dihedral : 19.606 170.773 2210 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1278 helix: 1.91 (0.22), residues: 540 sheet: 1.13 (0.37), residues: 186 loop : 0.62 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 680 TYR 0.011 0.001 TYR B 470 PHE 0.021 0.001 PHE D 731 TRP 0.023 0.002 TRP D 740 HIS 0.002 0.001 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00343 (11748) covalent geometry : angle 0.50621 (16232) hydrogen bonds : bond 0.04096 ( 498) hydrogen bonds : angle 3.84374 ( 1464) link_BETA1-4 : bond 0.00193 ( 4) link_BETA1-4 : angle 1.42445 ( 12) link_NAG-ASN : bond 0.00129 ( 6) link_NAG-ASN : angle 1.31082 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.442 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.7461 time to fit residues: 18.0301 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.052976 restraints weight = 60796.637| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.10 r_work: 0.2716 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11758 Z= 0.162 Angle : 0.508 5.831 16262 Z= 0.279 Chirality : 0.041 0.186 1840 Planarity : 0.003 0.037 1842 Dihedral : 19.595 170.658 2210 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.24), residues: 1278 helix: 1.91 (0.22), residues: 540 sheet: 1.15 (0.37), residues: 186 loop : 0.62 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 155 TYR 0.011 0.001 TYR B 470 PHE 0.020 0.001 PHE B 731 TRP 0.022 0.002 TRP D 740 HIS 0.002 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00373 (11748) covalent geometry : angle 0.50552 (16232) hydrogen bonds : bond 0.04111 ( 498) hydrogen bonds : angle 3.83228 ( 1464) link_BETA1-4 : bond 0.00200 ( 4) link_BETA1-4 : angle 1.43682 ( 12) link_NAG-ASN : bond 0.00131 ( 6) link_NAG-ASN : angle 1.32734 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.443 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.7528 time to fit residues: 18.2473 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.071719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.053801 restraints weight = 53598.078| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.95 r_work: 0.2742 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11758 Z= 0.124 Angle : 0.495 5.843 16262 Z= 0.273 Chirality : 0.041 0.199 1840 Planarity : 0.003 0.035 1842 Dihedral : 19.579 170.684 2210 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.25), residues: 1278 helix: 1.94 (0.22), residues: 542 sheet: 1.16 (0.37), residues: 186 loop : 0.67 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.011 0.001 TYR D 309 PHE 0.018 0.001 PHE D 731 TRP 0.023 0.002 TRP D 740 HIS 0.001 0.001 HIS D 684 Details of bonding type rmsd covalent geometry : bond 0.00282 (11748) covalent geometry : angle 0.49254 (16232) hydrogen bonds : bond 0.03959 ( 498) hydrogen bonds : angle 3.79495 ( 1464) link_BETA1-4 : bond 0.00243 ( 4) link_BETA1-4 : angle 1.37517 ( 12) link_NAG-ASN : bond 0.00172 ( 6) link_NAG-ASN : angle 1.31869 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.401 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.7533 time to fit residues: 18.2706 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 10 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.071688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.054029 restraints weight = 43136.906| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.69 r_work: 0.2757 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11758 Z= 0.138 Angle : 0.494 5.707 16262 Z= 0.272 Chirality : 0.041 0.185 1840 Planarity : 0.003 0.036 1842 Dihedral : 19.562 170.481 2210 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.25), residues: 1278 helix: 1.96 (0.23), residues: 540 sheet: 1.19 (0.37), residues: 186 loop : 0.66 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 155 TYR 0.010 0.001 TYR D 309 PHE 0.019 0.001 PHE B 731 TRP 0.022 0.002 TRP D 740 HIS 0.002 0.001 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00314 (11748) covalent geometry : angle 0.49103 (16232) hydrogen bonds : bond 0.03963 ( 498) hydrogen bonds : angle 3.77023 ( 1464) link_BETA1-4 : bond 0.00241 ( 4) link_BETA1-4 : angle 1.39225 ( 12) link_NAG-ASN : bond 0.00160 ( 6) link_NAG-ASN : angle 1.31656 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.414 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.7492 time to fit residues: 18.1627 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 126 optimal weight: 0.0040 chunk 94 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.053847 restraints weight = 51680.929| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.91 r_work: 0.2744 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11758 Z= 0.132 Angle : 0.492 5.660 16262 Z= 0.271 Chirality : 0.041 0.189 1840 Planarity : 0.003 0.036 1842 Dihedral : 19.562 170.533 2210 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.25), residues: 1278 helix: 1.98 (0.22), residues: 540 sheet: 1.20 (0.37), residues: 186 loop : 0.66 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 668 TYR 0.010 0.001 TYR D 309 PHE 0.019 0.001 PHE B 731 TRP 0.022 0.002 TRP D 740 HIS 0.002 0.001 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00299 (11748) covalent geometry : angle 0.48882 (16232) hydrogen bonds : bond 0.03952 ( 498) hydrogen bonds : angle 3.76545 ( 1464) link_BETA1-4 : bond 0.00235 ( 4) link_BETA1-4 : angle 1.38300 ( 12) link_NAG-ASN : bond 0.00159 ( 6) link_NAG-ASN : angle 1.31764 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3473.92 seconds wall clock time: 60 minutes 10.34 seconds (3610.34 seconds total)