Starting phenix.real_space_refine on Wed Sep 25 21:14:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/09_2024/7zqs_14874.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/09_2024/7zqs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/09_2024/7zqs_14874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/09_2024/7zqs_14874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/09_2024/7zqs_14874.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/09_2024/7zqs_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 12.99, per 1000 atoms: 1.14 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: 3.05 Conformation dependent library (CDL) restraints added in 2.6 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: 4.00 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: 4.28 Time building geometry restraints manager: 3.51 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: 0.00 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: 1.690 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 39.350 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.530 ------------------------------------------------------------------------------- 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 11748 Z= 0.265 Angle : 0.568 6.547 16232 Z= 0.325 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.204 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 1.6611 time to fit residues: 50.9043 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11748 Z= 0.313 Angle : 0.569 7.912 16232 Z= 0.313 Chirality : 0.044 0.289 1840 Planarity : 0.004 0.033 1842 Dihedral : 19.838 172.075 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 1.237 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 1.6045 time to fit residues: 39.4342 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11748 Z= 0.386 Angle : 0.583 6.552 16232 Z= 0.318 Chirality : 0.045 0.272 1840 Planarity : 0.004 0.040 1842 Dihedral : 19.833 172.277 2210 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: 1.40 (0.24), residues: 1278 helix: 1.55 (0.22), residues: 538 sheet: 1.02 (0.35), residues: 202 loop : 0.38 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 740 HIS 0.006 0.001 HIS B 603 PHE 0.019 0.002 PHE B 731 TYR 0.013 0.001 TYR B 470 ARG 0.003 0.000 ARG B 155 *********************** 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 fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.286 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4798 time to fit residues: 36.7206 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 0.0970 chunk 80 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11748 Z= 0.177 Angle : 0.498 6.335 16232 Z= 0.276 Chirality : 0.041 0.251 1840 Planarity : 0.003 0.033 1842 Dihedral : 19.605 171.296 2210 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: 1.87 (0.23), residues: 540 sheet: 1.06 (0.35), residues: 202 loop : 0.52 (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 D 603 PHE 0.019 0.001 PHE B 313 TYR 0.011 0.001 TYR D 309 ARG 0.002 0.000 ARG D 668 *********************** 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 fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.305 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4894 time to fit residues: 36.5399 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11748 Z= 0.342 Angle : 0.549 6.023 16232 Z= 0.301 Chirality : 0.044 0.217 1840 Planarity : 0.003 0.039 1842 Dihedral : 19.695 171.267 2210 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: 1.58 (0.24), residues: 1278 helix: 1.76 (0.22), residues: 538 sheet: 0.97 (0.37), residues: 186 loop : 0.50 (0.29), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 740 HIS 0.004 0.001 HIS D 603 PHE 0.018 0.002 PHE B 313 TYR 0.013 0.001 TYR B 470 ARG 0.002 0.000 ARG B 155 *********************** 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 fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.270 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.7833 time to fit residues: 43.9899 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11748 Z= 0.169 Angle : 0.492 5.788 16232 Z= 0.272 Chirality : 0.040 0.203 1840 Planarity : 0.003 0.035 1842 Dihedral : 19.566 170.797 2210 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.19 % Allowed : 3.14 % Favored : 96.67 % 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: 1.83 (0.24), residues: 1278 helix: 1.96 (0.22), residues: 540 sheet: 1.14 (0.35), residues: 202 loop : 0.60 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 740 HIS 0.002 0.001 HIS B 603 PHE 0.018 0.001 PHE D 313 TYR 0.010 0.001 TYR B 309 ARG 0.002 0.000 ARG D 623 *********************** 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 fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 1.251 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 1.4961 time to fit residues: 36.7820 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 127 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11748 Z= 0.185 Angle : 0.487 5.612 16232 Z= 0.270 Chirality : 0.041 0.196 1840 Planarity : 0.003 0.036 1842 Dihedral : 19.547 170.317 2210 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.98 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: 1.89 (0.24), residues: 1278 helix: 1.98 (0.22), residues: 542 sheet: 1.17 (0.37), residues: 186 loop : 0.68 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 740 HIS 0.002 0.001 HIS B 603 PHE 0.017 0.001 PHE D 313 TYR 0.010 0.001 TYR D 309 ARG 0.001 0.000 ARG D 668 *********************** 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 fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.415 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4671 time to fit residues: 36.0857 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 0.0470 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11748 Z= 0.198 Angle : 0.491 5.544 16232 Z= 0.272 Chirality : 0.041 0.195 1840 Planarity : 0.003 0.036 1842 Dihedral : 19.546 170.119 2210 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 1.89 (0.24), residues: 1278 helix: 1.97 (0.22), residues: 542 sheet: 1.17 (0.37), residues: 186 loop : 0.68 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 740 HIS 0.002 0.001 HIS B 603 PHE 0.019 0.001 PHE D 731 TYR 0.011 0.001 TYR D 309 ARG 0.001 0.000 ARG D 155 *********************** 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 24 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.261 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 1.4645 time to fit residues: 39.3466 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11748 Z= 0.152 Angle : 0.482 5.539 16232 Z= 0.267 Chirality : 0.040 0.202 1840 Planarity : 0.003 0.036 1842 Dihedral : 19.527 170.023 2210 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: 1.92 (0.25), residues: 1278 helix: 2.00 (0.22), residues: 542 sheet: 1.18 (0.37), residues: 186 loop : 0.71 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 740 HIS 0.002 0.001 HIS D 300 PHE 0.019 0.001 PHE B 731 TYR 0.011 0.001 TYR D 309 ARG 0.002 0.000 ARG D 623 *********************** 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 fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.199 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4813 time to fit residues: 36.5118 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 131 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11748 Z= 0.144 Angle : 0.477 5.469 16232 Z= 0.265 Chirality : 0.040 0.184 1840 Planarity : 0.003 0.037 1842 Dihedral : 19.511 169.852 2210 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: 1.96 (0.25), residues: 1278 helix: 2.01 (0.22), residues: 544 sheet: 1.21 (0.37), residues: 186 loop : 0.75 (0.30), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 740 HIS 0.002 0.001 HIS D 707 PHE 0.018 0.001 PHE B 731 TYR 0.011 0.001 TYR D 309 ARG 0.001 0.000 ARG B 732 ********************** 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 fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.214 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.5493 time to fit residues: 37.8998 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 15 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 5 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 = 0.070852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.052865 restraints weight = 53769.861| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.95 r_work: 0.2717 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11748 Z= 0.270 Angle : 0.517 5.819 16232 Z= 0.285 Chirality : 0.042 0.191 1840 Planarity : 0.003 0.041 1842 Dihedral : 19.582 169.934 2210 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: 1.85 (0.22), residues: 544 sheet: 1.11 (0.37), residues: 186 loop : 0.65 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 740 HIS 0.003 0.001 HIS D 603 PHE 0.022 0.001 PHE B 731 TYR 0.012 0.001 TYR B 470 ARG 0.002 0.000 ARG B 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.58 seconds wall clock time: 43 minutes 17.35 seconds (2597.35 seconds total)