Starting phenix.real_space_refine on Fri Mar 15 10:17:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/03_2024/7zqs_14874.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/03_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_14874/03_2024/7zqs_14874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/03_2024/7zqs_14874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/03_2024/7zqs_14874.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqs_14874/03_2024/7zqs_14874.pdb" } 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 Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "B PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 579": "NH1" <-> "NH2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B ARG 613": "NH1" <-> "NH2" Residue "B ARG 623": "NH1" <-> "NH2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B ARG 677": "NH1" <-> "NH2" Residue "B ARG 680": "NH1" <-> "NH2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B ARG 719": "NH1" <-> "NH2" Residue "B ARG 732": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 364": "NH1" <-> "NH2" Residue "D TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 446": "NH1" <-> "NH2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 579": "NH1" <-> "NH2" Residue "D ARG 588": "NH1" <-> "NH2" Residue "D ARG 613": "NH1" <-> "NH2" Residue "D ARG 623": "NH1" <-> "NH2" Residue "D ARG 629": "NH1" <-> "NH2" Residue "D ARG 646": "NH1" <-> "NH2" Residue "D ARG 651": "NH1" <-> "NH2" Residue "D ARG 655": "NH1" <-> "NH2" Residue "D ARG 668": "NH1" <-> "NH2" Residue "D ARG 677": "NH1" <-> "NH2" Residue "D ARG 680": "NH1" <-> "NH2" Residue "D ARG 698": "NH1" <-> "NH2" Residue "D ARG 719": "NH1" <-> "NH2" Residue "D ARG 732": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.06, per 1000 atoms: 0.97 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 5.26 Conformation dependent library (CDL) restraints added in 3.9 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: 4.26 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: 4.52 Time building geometry restraints manager: 5.62 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: 99.40 - 106.32: 660 106.32 - 113.25: 6426 113.25 - 120.17: 4066 120.17 - 127.09: 4797 127.09 - 134.01: 283 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 2.520 nonbonded pdb=" O LEU D 387 " pdb=" NH2 ARG D 409 " model vdw 2.268 2.520 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 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.100 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 45.460 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 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:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.900 ------------------------------------------------------------------------------- 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 : 1.260 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 1.7397 time to fit residues: 53.3042 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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: 3.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11748 Z= 0.337 Angle : 0.573 7.690 16232 Z= 0.313 Chirality : 0.044 0.292 1840 Planarity : 0.004 0.032 1842 Dihedral : 19.855 172.288 2210 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 1.44 (0.24), residues: 1278 helix: 1.59 (0.23), residues: 542 sheet: 1.10 (0.35), residues: 202 loop : 0.35 (0.29), residues: 534 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 B 731 TYR 0.012 0.001 TYR D 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 : 1.228 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 1.4628 time to fit residues: 35.9102 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.8777 moved from start: 0.0708 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= 0.264 Angle : 0.530 6.989 16232 Z= 0.291 Chirality : 0.042 0.262 1840 Planarity : 0.003 0.029 1842 Dihedral : 19.664 172.040 2210 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 1.73 (0.23), residues: 542 sheet: 1.14 (0.35), residues: 202 loop : 0.35 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 740 HIS 0.004 0.001 HIS B 603 PHE 0.019 0.002 PHE D 313 TYR 0.010 0.001 TYR D 470 ARG 0.003 0.000 ARG B 668 *********************** 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 : 1.195 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4972 time to fit residues: 36.7642 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11748 Z= 0.208 Angle : 0.513 6.718 16232 Z= 0.282 Chirality : 0.041 0.249 1840 Planarity : 0.003 0.027 1842 Dihedral : 19.611 171.960 2210 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 1.64 (0.24), residues: 1278 helix: 1.85 (0.23), residues: 540 sheet: 1.15 (0.35), residues: 202 loop : 0.39 (0.29), 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 0.018 0.001 PHE D 313 TYR 0.011 0.001 TYR D 309 ARG 0.002 0.000 ARG B 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 : 1.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4629 time to fit residues: 36.1513 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.8783 moved from start: 0.0827 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= 0.300 Angle : 0.533 6.302 16232 Z= 0.292 Chirality : 0.043 0.230 1840 Planarity : 0.003 0.029 1842 Dihedral : 19.643 171.892 2210 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 1.57 (0.24), residues: 1278 helix: 1.78 (0.22), residues: 540 sheet: 1.10 (0.35), residues: 202 loop : 0.37 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 740 HIS 0.004 0.001 HIS B 603 PHE 0.018 0.002 PHE D 313 TYR 0.012 0.001 TYR B 470 ARG 0.001 0.000 ARG B 698 *********************** 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 : 1.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4575 time to fit residues: 35.9052 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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: 2.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.8750 moved from start: 0.0931 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= 0.173 Angle : 0.490 6.087 16232 Z= 0.271 Chirality : 0.040 0.223 1840 Planarity : 0.003 0.026 1842 Dihedral : 19.549 171.493 2210 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 1.77 (0.24), residues: 1278 helix: 1.98 (0.23), residues: 540 sheet: 1.18 (0.35), residues: 202 loop : 0.44 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 740 HIS 0.002 0.001 HIS D 603 PHE 0.018 0.001 PHE D 313 TYR 0.010 0.001 TYR B 309 ARG 0.002 0.000 ARG D 668 *********************** 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 fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.165 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.4365 time to fit residues: 35.6118 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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: 10.0000 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.8772 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11748 Z= 0.279 Angle : 0.516 5.944 16232 Z= 0.284 Chirality : 0.042 0.209 1840 Planarity : 0.003 0.028 1842 Dihedral : 19.576 171.404 2210 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: 1.69 (0.24), residues: 1278 helix: 1.90 (0.23), residues: 540 sheet: 1.13 (0.35), residues: 202 loop : 0.42 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 740 HIS 0.003 0.001 HIS B 603 PHE 0.018 0.001 PHE D 313 TYR 0.011 0.001 TYR B 470 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 : 1.294 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.5199 time to fit residues: 37.5068 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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: 3.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8737 moved from start: 0.1038 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= 0.157 Angle : 0.479 5.881 16232 Z= 0.265 Chirality : 0.040 0.216 1840 Planarity : 0.003 0.027 1842 Dihedral : 19.493 171.048 2210 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.24), residues: 1278 helix: 2.07 (0.23), residues: 540 sheet: 1.20 (0.35), residues: 202 loop : 0.48 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 740 HIS 0.002 0.001 HIS D 603 PHE 0.018 0.001 PHE D 313 TYR 0.010 0.001 TYR B 309 ARG 0.002 0.000 ARG B 668 *********************** 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 23 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.313 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 1.6160 time to fit residues: 41.4139 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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: 4.9990 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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: 0.8783 moved from start: 0.0955 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= 0.328 Angle : 0.533 5.915 16232 Z= 0.292 Chirality : 0.043 0.203 1840 Planarity : 0.003 0.030 1842 Dihedral : 19.593 171.270 2210 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 1.66 (0.24), residues: 1278 helix: 1.87 (0.22), residues: 540 sheet: 1.10 (0.37), residues: 186 loop : 0.44 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 740 HIS 0.004 0.001 HIS D 603 PHE 0.018 0.002 PHE D 313 TYR 0.012 0.001 TYR B 470 ARG 0.001 0.000 ARG D 668 *********************** 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 : 1.285 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.5414 time to fit residues: 39.0410 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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: 0.9980 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 111 optimal weight: 0.0470 chunk 32 optimal weight: 0.0970 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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: 0.8706 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11748 Z= 0.133 Angle : 0.468 5.782 16232 Z= 0.259 Chirality : 0.039 0.202 1840 Planarity : 0.003 0.027 1842 Dihedral : 19.424 170.906 2210 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 1.99 (0.24), residues: 1278 helix: 2.13 (0.23), residues: 542 sheet: 1.47 (0.37), residues: 182 loop : 0.54 (0.29), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 740 HIS 0.002 0.000 HIS B 186 PHE 0.017 0.001 PHE D 313 TYR 0.009 0.001 TYR B 309 ARG 0.001 0.000 ARG B 155 ********************** 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 27 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 1.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 1.6456 time to fit residues: 48.8876 Evaluate side-chains 22 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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: 0.4980 chunk 29 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 107 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 0.0020 chunk 5 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.072068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.054143 restraints weight = 53467.030| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.96 r_work: 0.2747 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1193 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= 0.191 Angle : 0.479 5.538 16232 Z= 0.264 Chirality : 0.040 0.194 1840 Planarity : 0.003 0.029 1842 Dihedral : 19.469 170.511 2210 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: 1.97 (0.24), residues: 1278 helix: 2.10 (0.23), residues: 542 sheet: 1.31 (0.35), residues: 202 loop : 0.59 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 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 B 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2368.46 seconds wall clock time: 43 minutes 42.06 seconds (2622.06 seconds total)