Starting phenix.real_space_refine on Tue Jul 29 10:34:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zqs_14874/07_2025/7zqs_14874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zqs_14874/07_2025/7zqs_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_14874/07_2025/7zqs_14874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zqs_14874/07_2025/7zqs_14874.map" model { file = "/net/cci-nas-00/data/ceres_data/7zqs_14874/07_2025/7zqs_14874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zqs_14874/07_2025/7zqs_14874.cif" } resolution = 2.54 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= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} 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: 11.99, per 1000 atoms: 1.06 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: 3.21 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 4.39 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: 4.46 Time building geometry restraints manager: 3.75 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: 0.06 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 758 or resid 801)) selection = (chain 'D' and (resid 120 through 639 or resid 641 through 758 or resid 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 40.000 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (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 TRP 0.027 0.002 TRP D 740 HIS 0.004 0.001 HIS B 603 PHE 0.019 0.002 PHE D 313 TYR 0.013 0.001 TYR D 309 ARG 0.003 0.000 ARG B 623 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 6) link_NAG-ASN : angle 1.33549 ( 18) link_BETA1-4 : bond 0.00265 ( 4) link_BETA1-4 : angle 2.02082 ( 12) hydrogen bonds : bond 0.15010 ( 498) hydrogen bonds : angle 5.85480 ( 1464) covalent geometry : bond 0.00421 (11748) covalent geometry : angle 0.56841 (16232) *********************** 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 : 1.155 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 1.8002 time to fit residues: 55.0552 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 : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.069935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.052358 restraints weight = 40384.842| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.60 r_work: 0.2713 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11758 Z= 0.217 Angle : 0.572 7.909 16262 Z= 0.313 Chirality : 0.044 0.289 1840 Planarity : 0.004 0.033 1842 Dihedral : 19.838 172.076 2210 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.19 % Allowed : 1.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1278 helix: 1.61 (0.22), residues: 540 sheet: 1.07 (0.36), residues: 194 loop : 0.43 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 740 HIS 0.005 0.001 HIS B 603 PHE 0.019 0.002 PHE D 313 TYR 0.011 0.001 TYR B 470 ARG 0.004 0.000 ARG D 668 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 6) link_NAG-ASN : angle 1.30959 ( 18) link_BETA1-4 : bond 0.00033 ( 4) link_BETA1-4 : angle 1.49639 ( 12) hydrogen bonds : bond 0.05476 ( 498) hydrogen bonds : angle 4.42008 ( 1464) covalent geometry : bond 0.00501 (11748) covalent geometry : angle 0.56945 (16232) *********************** 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 24 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 1.164 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 1.4839 time to fit residues: 36.4058 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 : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.070339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.052634 restraints weight = 45017.418| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.73 r_work: 0.2715 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11758 Z= 0.183 Angle : 0.546 6.838 16262 Z= 0.298 Chirality : 0.043 0.282 1840 Planarity : 0.003 0.034 1842 Dihedral : 19.781 172.032 2210 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1278 helix: 1.71 (0.22), residues: 540 sheet: 1.04 (0.35), residues: 202 loop : 0.43 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 740 HIS 0.004 0.001 HIS D 603 PHE 0.018 0.002 PHE D 313 TYR 0.011 0.001 TYR D 309 ARG 0.003 0.000 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 6) link_NAG-ASN : angle 1.35250 ( 18) link_BETA1-4 : bond 0.00120 ( 4) link_BETA1-4 : angle 1.39555 ( 12) hydrogen bonds : bond 0.04817 ( 498) hydrogen bonds : angle 4.12193 ( 1464) covalent geometry : bond 0.00423 (11748) covalent geometry : angle 0.54303 (16232) *********************** 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 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 1.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.5241 time to fit residues: 37.5563 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 : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 38 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.068939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.051005 restraints weight = 53229.527| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.94 r_work: 0.2667 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11758 Z= 0.277 Angle : 0.588 6.454 16262 Z= 0.319 Chirality : 0.046 0.240 1840 Planarity : 0.004 0.041 1842 Dihedral : 19.806 172.351 2210 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1278 helix: 1.58 (0.22), residues: 538 sheet: 0.73 (0.32), residues: 226 loop : 0.42 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 740 HIS 0.005 0.001 HIS D 603 PHE 0.019 0.002 PHE B 731 TYR 0.014 0.001 TYR B 470 ARG 0.003 0.000 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 6) link_NAG-ASN : angle 1.44566 ( 18) link_BETA1-4 : bond 0.00105 ( 4) link_BETA1-4 : angle 1.57885 ( 12) hydrogen bonds : bond 0.04964 ( 498) hydrogen bonds : angle 4.18076 ( 1464) covalent geometry : bond 0.00646 (11748) covalent geometry : angle 0.58458 (16232) *********************** 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 : 1.224 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4829 time to fit residues: 36.4872 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 : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.070971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053372 restraints weight = 42528.709| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.68 r_work: 0.2740 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 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 = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1005 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= 0.142 Angle : 0.509 6.152 16262 Z= 0.280 Chirality : 0.041 0.218 1840 Planarity : 0.003 0.036 1842 Dihedral : 19.637 171.547 2210 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1278 helix: 1.83 (0.23), residues: 540 sheet: 1.04 (0.34), residues: 202 loop : 0.45 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 740 HIS 0.003 0.001 HIS D 603 PHE 0.019 0.001 PHE D 313 TYR 0.010 0.001 TYR D 309 ARG 0.002 0.000 ARG D 668 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 6) link_NAG-ASN : angle 1.38174 ( 18) link_BETA1-4 : bond 0.00200 ( 4) link_BETA1-4 : angle 1.36288 ( 12) hydrogen bonds : bond 0.04279 ( 498) hydrogen bonds : angle 3.92935 ( 1464) covalent geometry : bond 0.00325 (11748) covalent geometry : angle 0.50594 (16232) *********************** 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 : 1.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4929 time to fit residues: 36.8375 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 : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.071046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.053612 restraints weight = 38325.609| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.54 r_work: 0.2751 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 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 = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1059 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 : 0.506 5.840 16262 Z= 0.278 Chirality : 0.041 0.216 1840 Planarity : 0.003 0.037 1842 Dihedral : 19.616 171.066 2210 Min Nonbonded Distance : 2.199 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1278 helix: 1.89 (0.22), residues: 540 sheet: 1.05 (0.34), residues: 202 loop : 0.53 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 740 HIS 0.002 0.001 HIS B 603 PHE 0.018 0.001 PHE B 313 TYR 0.011 0.001 TYR B 309 ARG 0.002 0.000 ARG B 668 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 6) link_NAG-ASN : angle 1.34100 ( 18) link_BETA1-4 : bond 0.00207 ( 4) link_BETA1-4 : angle 1.41657 ( 12) hydrogen bonds : bond 0.04185 ( 498) hydrogen bonds : angle 3.87576 ( 1464) covalent geometry : bond 0.00339 (11748) covalent geometry : angle 0.50336 (16232) *********************** 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 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 1.140 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4793 time to fit residues: 36.5527 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 : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 35 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.071490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.053976 restraints weight = 41132.947| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.63 r_work: 0.2757 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 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 = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1105 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= 0.125 Angle : 0.495 5.777 16262 Z= 0.273 Chirality : 0.041 0.202 1840 Planarity : 0.003 0.035 1842 Dihedral : 19.594 170.889 2210 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1278 helix: 1.93 (0.22), residues: 540 sheet: 1.11 (0.35), residues: 202 loop : 0.55 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 740 HIS 0.001 0.001 HIS D 707 PHE 0.018 0.001 PHE D 313 TYR 0.011 0.001 TYR B 309 ARG 0.002 0.000 ARG D 668 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 6) link_NAG-ASN : angle 1.32936 ( 18) link_BETA1-4 : bond 0.00247 ( 4) link_BETA1-4 : angle 1.39697 ( 12) hydrogen bonds : bond 0.04053 ( 498) hydrogen bonds : angle 3.83438 ( 1464) covalent geometry : bond 0.00277 (11748) covalent geometry : angle 0.49218 (16232) *********************** 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 : 1.155 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4426 time to fit residues: 35.5977 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 : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.0980 chunk 94 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.070593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.052431 restraints weight = 62434.697| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.14 r_work: 0.2700 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1077 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= 0.181 Angle : 0.517 5.668 16262 Z= 0.284 Chirality : 0.042 0.194 1840 Planarity : 0.003 0.037 1842 Dihedral : 19.613 170.657 2210 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1278 helix: 1.86 (0.22), residues: 540 sheet: 1.07 (0.37), residues: 186 loop : 0.56 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 740 HIS 0.003 0.001 HIS D 603 PHE 0.018 0.001 PHE B 313 TYR 0.011 0.001 TYR B 309 ARG 0.002 0.000 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00122 ( 6) link_NAG-ASN : angle 1.35191 ( 18) link_BETA1-4 : bond 0.00178 ( 4) link_BETA1-4 : angle 1.48248 ( 12) hydrogen bonds : bond 0.04213 ( 498) hydrogen bonds : angle 3.87493 ( 1464) covalent geometry : bond 0.00421 (11748) covalent geometry : angle 0.51442 (16232) *********************** 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 : 1.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.7883 time to fit residues: 43.7400 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 : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 51 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.072851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.055144 restraints weight = 47926.158| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.82 r_work: 0.2781 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11758 Z= 0.109 Angle : 0.475 5.582 16262 Z= 0.263 Chirality : 0.040 0.193 1840 Planarity : 0.003 0.035 1842 Dihedral : 19.506 170.157 2210 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1278 helix: 2.04 (0.23), residues: 542 sheet: 1.21 (0.37), residues: 186 loop : 0.68 (0.30), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 740 HIS 0.002 0.000 HIS D 186 PHE 0.017 0.001 PHE D 313 TYR 0.009 0.001 TYR B 309 ARG 0.002 0.000 ARG B 680 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 6) link_NAG-ASN : angle 1.33487 ( 18) link_BETA1-4 : bond 0.00273 ( 4) link_BETA1-4 : angle 1.30565 ( 12) hydrogen bonds : bond 0.03749 ( 498) hydrogen bonds : angle 3.70483 ( 1464) covalent geometry : bond 0.00238 (11748) covalent geometry : angle 0.47221 (16232) *********************** 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 : 1.696 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 2.0325 time to fit residues: 49.7306 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 : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 0.0060 chunk 59 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.072924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.055147 restraints weight = 51362.851| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.89 r_work: 0.2779 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 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 = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11758 Z= 0.110 Angle : 0.471 5.278 16262 Z= 0.260 Chirality : 0.040 0.182 1840 Planarity : 0.003 0.039 1842 Dihedral : 19.496 169.690 2210 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.25), residues: 1278 helix: 2.12 (0.23), residues: 542 sheet: 1.30 (0.37), residues: 186 loop : 0.73 (0.30), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 740 HIS 0.002 0.000 HIS B 300 PHE 0.016 0.001 PHE B 313 TYR 0.010 0.001 TYR B 309 ARG 0.002 0.000 ARG D 680 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 6) link_NAG-ASN : angle 1.28795 ( 18) link_BETA1-4 : bond 0.00257 ( 4) link_BETA1-4 : angle 1.36897 ( 12) hydrogen bonds : bond 0.03666 ( 498) hydrogen bonds : angle 3.68230 ( 1464) covalent geometry : bond 0.00241 (11748) covalent geometry : angle 0.46783 (16232) ********************** 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 23 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 1.249 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 1.4855 time to fit residues: 38.1210 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 : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.072969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.055180 restraints weight = 48222.341| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.83 r_work: 0.2782 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 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 = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1407 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= 0.116 Angle : 0.472 5.389 16262 Z= 0.261 Chirality : 0.040 0.191 1840 Planarity : 0.003 0.039 1842 Dihedral : 19.487 169.595 2210 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.25), residues: 1278 helix: 2.13 (0.23), residues: 542 sheet: 1.29 (0.37), residues: 186 loop : 0.74 (0.30), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 740 HIS 0.001 0.001 HIS D 707 PHE 0.017 0.001 PHE B 313 TYR 0.011 0.001 TYR D 309 ARG 0.001 0.000 ARG B 623 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 6) link_NAG-ASN : angle 1.25221 ( 18) link_BETA1-4 : bond 0.00268 ( 4) link_BETA1-4 : angle 1.36449 ( 12) hydrogen bonds : bond 0.03668 ( 498) hydrogen bonds : angle 3.66352 ( 1464) covalent geometry : bond 0.00257 (11748) covalent geometry : angle 0.46917 (16232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7116.33 seconds wall clock time: 125 minutes 33.08 seconds (7533.08 seconds total)