Starting phenix.real_space_refine on Thu Jun 27 19:03:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/06_2024/8xc1_38236_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/06_2024/8xc1_38236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/06_2024/8xc1_38236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/06_2024/8xc1_38236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/06_2024/8xc1_38236_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/06_2024/8xc1_38236_updated.pdb" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.102 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 Zn 2 6.06 5 P 122 5.49 5 S 68 5.16 5 C 8346 2.51 5 N 2224 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 714": "OD1" <-> "OD2" Residue "A ASP 764": "OD1" <-> "OD2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 714": "OD1" <-> "OD2" Residue "B ASP 764": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13542 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5257 Classifications: {'peptide': 660} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 654 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "D" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 625 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "B" Number of atoms: 5257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5257 Classifications: {'peptide': 660} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 654 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "F" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 625 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 27} 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: "I" 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: "J" 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: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.75, per 1000 atoms: 0.57 Number of scatterers: 13542 At special positions: 0 Unit cell: (120.157, 111.497, 130.982, 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) Zn 2 29.99 S 68 16.00 P 122 15.00 O 2780 8.00 N 2224 7.00 C 8346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 731 " distance=2.03 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 5.50 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 744 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 540 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 744 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 740 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 540 " 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 8 sheets defined 43.3% alpha, 14.5% beta 28 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 5.89 Creating SS restraints... Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 128 through 131 Processing helix chain 'A' and resid 206 through 209 No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 315 through 333 Proline residue: A 328 - end of helix removed outlier: 4.779A pdb=" N LEU A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 427 through 430 No H-bonds generated for 'chain 'A' and resid 427 through 430' Processing helix chain 'A' and resid 436 through 453 Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 457 through 463 removed outlier: 3.903A pdb=" N ASP A 461 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 480 through 503 removed outlier: 4.786A pdb=" N ASN A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLY A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 541 removed outlier: 3.667A pdb=" N ILE A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 577 through 595 Processing helix chain 'A' and resid 602 through 625 Processing helix chain 'A' and resid 632 through 651 Processing helix chain 'A' and resid 658 through 683 removed outlier: 4.817A pdb=" N ALA A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N THR A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 739 through 765 removed outlier: 4.994A pdb=" N ASP A 762 " --> pdb=" O VAL A 758 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 765 " --> pdb=" O VAL A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 81 through 84 Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 206 through 209 No H-bonds generated for 'chain 'B' and resid 206 through 209' Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 315 through 333 Proline residue: B 328 - end of helix removed outlier: 4.779A pdb=" N LEU B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 427 through 430 No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 436 through 453 Proline residue: B 440 - end of helix Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.904A pdb=" N ASP B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 480 through 503 removed outlier: 4.786A pdb=" N ASN B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLY B 488 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 541 removed outlier: 3.667A pdb=" N ILE B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 577 through 595 Processing helix chain 'B' and resid 602 through 625 Processing helix chain 'B' and resid 632 through 651 Processing helix chain 'B' and resid 658 through 683 removed outlier: 4.817A pdb=" N ALA B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N THR B 663 " --> pdb=" O ASN B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 711 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 739 through 765 removed outlier: 4.994A pdb=" N ASP B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP B 763 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP B 764 " --> pdb=" O PHE B 760 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU B 765 " --> pdb=" O VAL B 761 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.497A pdb=" N VAL A 56 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE A 38 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 58 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 46 through 51 removed outlier: 3.918A pdb=" N THR A 72 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.700A pdb=" N GLN A 213 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 200 through 205 Processing sheet with id= E, first strand: chain 'B' and resid 35 through 39 removed outlier: 6.498A pdb=" N VAL B 56 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE B 38 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 58 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.918A pdb=" N THR B 72 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 186 through 189 removed outlier: 3.700A pdb=" N GLN B 213 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 200 through 205 516 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 5.01 Time building geometry restraints manager: 6.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2093 1.33 - 1.45: 4350 1.45 - 1.57: 7315 1.57 - 1.69: 240 1.69 - 1.81: 102 Bond restraints: 14100 Sorted by residual: bond pdb=" CA ARG B 240 " pdb=" CB ARG B 240 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" CA ARG A 240 " pdb=" CB ARG A 240 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" CD ARG B 240 " pdb=" NE ARG B 240 " ideal model delta sigma weight residual 1.458 1.400 0.058 1.40e-02 5.10e+03 1.74e+01 bond pdb=" CD ARG A 240 " pdb=" NE ARG A 240 " ideal model delta sigma weight residual 1.458 1.400 0.058 1.40e-02 5.10e+03 1.74e+01 bond pdb=" N PRO B 143 " pdb=" CD PRO B 143 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.33e+01 ... (remaining 14095 not shown) Histogram of bond angle deviations from ideal: 75.84 - 91.08: 11 91.08 - 106.32: 947 106.32 - 121.56: 15630 121.56 - 136.80: 3114 136.80 - 152.05: 2 Bond angle restraints: 19704 Sorted by residual: angle pdb=" N ALA A 133 " pdb=" CA ALA A 133 " pdb=" C ALA A 133 " ideal model delta sigma weight residual 112.87 152.05 -39.18 1.20e+00 6.94e-01 1.07e+03 angle pdb=" N ALA B 133 " pdb=" CA ALA B 133 " pdb=" C ALA B 133 " ideal model delta sigma weight residual 112.87 152.05 -39.18 1.20e+00 6.94e-01 1.07e+03 angle pdb=" C SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta sigma weight residual 110.74 75.84 34.90 1.61e+00 3.86e-01 4.70e+02 angle pdb=" C SER A 244 " pdb=" CA SER A 244 " pdb=" CB SER A 244 " ideal model delta sigma weight residual 110.74 75.84 34.90 1.61e+00 3.86e-01 4.70e+02 angle pdb=" C ILE B 243 " pdb=" CA ILE B 243 " pdb=" CB ILE B 243 " ideal model delta sigma weight residual 111.88 132.49 -20.61 1.28e+00 6.10e-01 2.59e+02 ... (remaining 19699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 8258 35.50 - 71.01: 684 71.01 - 106.51: 116 106.51 - 142.01: 30 142.01 - 177.51: 8 Dihedral angle restraints: 9096 sinusoidal: 5210 harmonic: 3886 Sorted by residual: dihedral pdb=" C SER B 244 " pdb=" N SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta harmonic sigma weight residual -122.60 -75.99 -46.61 0 2.50e+00 1.60e-01 3.48e+02 dihedral pdb=" C SER A 244 " pdb=" N SER A 244 " pdb=" CA SER A 244 " pdb=" CB SER A 244 " ideal model delta harmonic sigma weight residual -122.60 -75.99 -46.61 0 2.50e+00 1.60e-01 3.48e+02 dihedral pdb=" C ILE B 243 " pdb=" N ILE B 243 " pdb=" CA ILE B 243 " pdb=" CB ILE B 243 " ideal model delta harmonic sigma weight residual -122.00 -164.90 42.90 0 2.50e+00 1.60e-01 2.94e+02 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.334: 2388 0.334 - 0.669: 15 0.669 - 1.003: 3 1.003 - 1.338: 0 1.338 - 1.672: 4 Chirality restraints: 2410 Sorted by residual: chirality pdb=" CA ILE B 243 " pdb=" N ILE B 243 " pdb=" C ILE B 243 " pdb=" CB ILE B 243 " both_signs ideal model delta sigma weight residual False 2.43 0.76 1.67 2.00e-01 2.50e+01 6.99e+01 chirality pdb=" CA ILE A 243 " pdb=" N ILE A 243 " pdb=" C ILE A 243 " pdb=" CB ILE A 243 " both_signs ideal model delta sigma weight residual False 2.43 0.76 1.67 2.00e-01 2.50e+01 6.99e+01 chirality pdb=" CA ALA B 133 " pdb=" N ALA B 133 " pdb=" C ALA B 133 " pdb=" CB ALA B 133 " both_signs ideal model delta sigma weight residual False 2.48 1.07 1.41 2.00e-01 2.50e+01 4.99e+01 ... (remaining 2407 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 807 " -0.168 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG B 807 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B 807 " -0.124 2.00e-02 2.50e+03 pdb=" N2 NAG B 807 " 0.224 2.00e-02 2.50e+03 pdb=" O7 NAG B 807 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 807 " -0.168 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG A 807 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG A 807 " -0.124 2.00e-02 2.50e+03 pdb=" N2 NAG A 807 " 0.224 2.00e-02 2.50e+03 pdb=" O7 NAG A 807 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 142 " 0.080 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO B 143 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " 0.060 5.00e-02 4.00e+02 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 62 2.47 - 3.08: 8676 3.08 - 3.69: 21056 3.69 - 4.29: 32276 4.29 - 4.90: 50399 Nonbonded interactions: 112469 Sorted by model distance: nonbonded pdb=" O SER A 244 " pdb=" CB SER A 244 " model vdw 1.869 2.752 nonbonded pdb=" O SER B 244 " pdb=" CB SER B 244 " model vdw 1.869 2.752 nonbonded pdb=" O HIS B 138 " pdb=" CB HIS B 138 " model vdw 2.186 2.752 nonbonded pdb=" O2' C E 11 " pdb=" O5' G E 12 " model vdw 2.257 2.440 nonbonded pdb=" O2' C C 11 " pdb=" O5' G C 12 " model vdw 2.257 2.440 ... (remaining 112464 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 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=1.00 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: 1.190 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: 4.060 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 43.070 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.120 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 0.103 14100 Z= 0.256 Angle : 1.194 39.176 19704 Z= 0.731 Chirality : 0.091 1.672 2410 Planarity : 0.008 0.139 1946 Dihedral : 24.883 177.515 6546 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.05 % Allowed : 23.55 % Favored : 74.40 % Cbeta Deviations : 1.66 % Peptide Plane: Cis-proline : 5.56 % 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: 1.19 (0.24), residues: 1308 helix: 2.42 (0.22), residues: 532 sheet: 1.94 (0.32), residues: 264 loop : -1.79 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 567 HIS 0.003 0.001 HIS B 540 PHE 0.012 0.001 PHE A 103 TYR 0.019 0.001 TYR A 650 ARG 0.016 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8179 (tp30) REVERT: A 272 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7901 (mtmm) REVERT: B 221 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8195 (tp30) REVERT: B 272 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7899 (mtmm) REVERT: B 604 PHE cc_start: 0.8417 (m-80) cc_final: 0.8208 (m-80) outliers start: 24 outliers final: 17 residues processed: 155 average time/residue: 1.0286 time to fit residues: 177.0369 Evaluate side-chains 148 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 84 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 210 ASN A 215 HIS A 227 ASN B 138 HIS B 210 ASN B 215 HIS B 227 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 14100 Z= 0.453 Angle : 0.823 9.482 19704 Z= 0.407 Chirality : 0.050 0.231 2410 Planarity : 0.006 0.072 1946 Dihedral : 24.712 172.899 4154 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.28 % Favored : 95.57 % Rotamer: Outliers : 5.80 % Allowed : 20.31 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1308 helix: 1.57 (0.22), residues: 546 sheet: 1.63 (0.32), residues: 262 loop : -1.65 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 452 HIS 0.009 0.002 HIS A 134 PHE 0.026 0.003 PHE B 528 TYR 0.024 0.003 TYR A 650 ARG 0.006 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 123 time to evaluate : 1.270 Fit side-chains REVERT: A 221 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8156 (tp30) REVERT: A 246 LYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6052 (ptpp) REVERT: A 674 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7567 (mp) REVERT: B 246 LYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6068 (ptpp) REVERT: B 674 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7570 (mp) outliers start: 68 outliers final: 37 residues processed: 169 average time/residue: 0.9611 time to fit residues: 181.5295 Evaluate side-chains 161 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14100 Z= 0.148 Angle : 0.646 9.440 19704 Z= 0.315 Chirality : 0.042 0.235 2410 Planarity : 0.004 0.059 1946 Dihedral : 22.933 173.045 4146 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.58 % Allowed : 22.78 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.03 (0.24), residues: 1308 helix: 1.86 (0.22), residues: 548 sheet: 1.96 (0.32), residues: 262 loop : -1.48 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 567 HIS 0.002 0.001 HIS A 571 PHE 0.011 0.001 PHE A 103 TYR 0.022 0.001 TYR B 650 ARG 0.002 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 1.307 Fit side-chains REVERT: A 246 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.6068 (pmtt) REVERT: A 430 MET cc_start: 0.6810 (mtp) cc_final: 0.6554 (mtp) REVERT: B 246 LYS cc_start: 0.6289 (OUTLIER) cc_final: 0.6057 (ptpp) REVERT: B 430 MET cc_start: 0.6805 (mtp) cc_final: 0.6552 (mtp) outliers start: 42 outliers final: 20 residues processed: 158 average time/residue: 0.9451 time to fit residues: 166.7093 Evaluate side-chains 150 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 131 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14100 Z= 0.366 Angle : 0.731 8.951 19704 Z= 0.363 Chirality : 0.047 0.220 2410 Planarity : 0.005 0.066 1946 Dihedral : 22.540 174.129 4144 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.78 % Allowed : 21.76 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1308 helix: 1.60 (0.22), residues: 546 sheet: 1.75 (0.32), residues: 262 loop : -1.68 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 567 HIS 0.006 0.001 HIS B 540 PHE 0.024 0.002 PHE B 528 TYR 0.021 0.002 TYR B 650 ARG 0.005 0.001 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 125 time to evaluate : 1.236 Fit side-chains REVERT: A 246 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5976 (ptpp) REVERT: A 674 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7549 (mp) REVERT: B 246 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5983 (ptpp) REVERT: B 674 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7551 (mp) outliers start: 56 outliers final: 35 residues processed: 166 average time/residue: 1.0237 time to fit residues: 189.7781 Evaluate side-chains 161 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 122 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 57 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14100 Z= 0.188 Angle : 0.605 8.318 19704 Z= 0.304 Chirality : 0.042 0.246 2410 Planarity : 0.004 0.063 1946 Dihedral : 21.995 173.729 4144 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.10 % Allowed : 22.18 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.02 (0.24), residues: 1308 helix: 2.07 (0.22), residues: 524 sheet: 1.97 (0.32), residues: 262 loop : -1.60 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 567 HIS 0.003 0.001 HIS B 571 PHE 0.013 0.001 PHE B 103 TYR 0.021 0.002 TYR A 650 ARG 0.002 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 127 time to evaluate : 1.219 Fit side-chains REVERT: A 430 MET cc_start: 0.6763 (mtp) cc_final: 0.6542 (mtp) REVERT: A 674 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7551 (mp) REVERT: B 430 MET cc_start: 0.6762 (mtp) cc_final: 0.6545 (mtp) REVERT: B 674 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7592 (mp) outliers start: 48 outliers final: 24 residues processed: 160 average time/residue: 1.0597 time to fit residues: 188.2264 Evaluate side-chains 153 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 34 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14100 Z= 0.266 Angle : 0.668 9.207 19704 Z= 0.334 Chirality : 0.044 0.225 2410 Planarity : 0.004 0.063 1946 Dihedral : 21.909 174.619 4136 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.20 % Favored : 95.64 % Rotamer: Outliers : 4.10 % Allowed : 22.27 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1308 helix: 1.98 (0.22), residues: 524 sheet: 1.81 (0.32), residues: 262 loop : -1.68 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 567 HIS 0.005 0.001 HIS B 540 PHE 0.020 0.002 PHE A 528 TYR 0.021 0.002 TYR A 650 ARG 0.004 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 124 time to evaluate : 1.237 Fit side-chains REVERT: A 430 MET cc_start: 0.6803 (mtp) cc_final: 0.6573 (mtp) REVERT: A 674 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7580 (mp) REVERT: B 430 MET cc_start: 0.6802 (mtp) cc_final: 0.6574 (mtp) REVERT: B 674 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7581 (mp) outliers start: 48 outliers final: 33 residues processed: 157 average time/residue: 0.9519 time to fit residues: 167.4229 Evaluate side-chains 154 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 138 optimal weight: 30.0000 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14100 Z= 0.169 Angle : 0.583 6.870 19704 Z= 0.292 Chirality : 0.041 0.259 2410 Planarity : 0.004 0.063 1946 Dihedral : 21.522 173.237 4134 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.41 % Allowed : 22.95 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.22 (0.24), residues: 1308 helix: 2.21 (0.22), residues: 516 sheet: 2.02 (0.32), residues: 264 loop : -1.38 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 567 HIS 0.003 0.001 HIS A 540 PHE 0.012 0.001 PHE B 103 TYR 0.021 0.001 TYR A 650 ARG 0.003 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.277 Fit side-chains REVERT: A 272 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7749 (mtmm) REVERT: A 430 MET cc_start: 0.6752 (mtp) cc_final: 0.6534 (mtp) REVERT: A 674 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7521 (mp) REVERT: B 272 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7749 (mtmm) REVERT: B 312 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7280 (mt0) REVERT: B 430 MET cc_start: 0.6750 (mtp) cc_final: 0.6534 (mtp) REVERT: B 674 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7521 (mp) outliers start: 40 outliers final: 24 residues processed: 154 average time/residue: 1.0546 time to fit residues: 181.0007 Evaluate side-chains 152 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14100 Z= 0.273 Angle : 0.653 7.138 19704 Z= 0.325 Chirality : 0.043 0.244 2410 Planarity : 0.004 0.064 1946 Dihedral : 21.506 174.843 4128 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.84 % Allowed : 22.27 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.00 (0.23), residues: 1308 helix: 2.11 (0.22), residues: 512 sheet: 1.80 (0.32), residues: 262 loop : -1.49 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.005 0.001 HIS B 540 PHE 0.021 0.002 PHE A 528 TYR 0.021 0.002 TYR A 650 ARG 0.004 0.001 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 126 time to evaluate : 1.301 Fit side-chains REVERT: A 208 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: A 430 MET cc_start: 0.6775 (mtp) cc_final: 0.6546 (mtp) REVERT: A 674 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 430 MET cc_start: 0.6775 (mtp) cc_final: 0.6547 (mtp) REVERT: B 674 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7598 (mp) outliers start: 45 outliers final: 30 residues processed: 159 average time/residue: 1.0201 time to fit residues: 180.4116 Evaluate side-chains 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 0.2980 chunk 39 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14100 Z= 0.215 Angle : 0.614 6.642 19704 Z= 0.306 Chirality : 0.041 0.236 2410 Planarity : 0.004 0.065 1946 Dihedral : 21.420 174.450 4128 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.33 % Allowed : 22.78 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.06 (0.23), residues: 1308 helix: 2.14 (0.22), residues: 512 sheet: 1.88 (0.32), residues: 262 loop : -1.47 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 567 HIS 0.004 0.001 HIS B 540 PHE 0.015 0.002 PHE B 103 TYR 0.021 0.001 TYR B 650 ARG 0.003 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 126 time to evaluate : 1.302 Fit side-chains REVERT: A 272 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7773 (mtmm) REVERT: A 430 MET cc_start: 0.6751 (mtp) cc_final: 0.6537 (mtp) REVERT: A 674 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7563 (mp) REVERT: B 272 LYS cc_start: 0.8282 (mtpp) cc_final: 0.7774 (mtmm) REVERT: B 430 MET cc_start: 0.6756 (mtp) cc_final: 0.6543 (mtp) REVERT: B 674 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7604 (mp) outliers start: 39 outliers final: 30 residues processed: 154 average time/residue: 1.0311 time to fit residues: 176.8407 Evaluate side-chains 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 88 optimal weight: 0.4980 chunk 70 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14100 Z= 0.201 Angle : 0.600 7.039 19704 Z= 0.298 Chirality : 0.041 0.255 2410 Planarity : 0.004 0.064 1946 Dihedral : 21.145 174.294 4128 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.24 % Allowed : 23.04 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.15 (0.24), residues: 1308 helix: 2.21 (0.22), residues: 512 sheet: 1.94 (0.32), residues: 264 loop : -1.44 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.003 0.001 HIS A 540 PHE 0.018 0.002 PHE B 711 TYR 0.022 0.001 TYR B 650 ARG 0.003 0.000 ARG B 570 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 1.126 Fit side-chains REVERT: A 272 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7769 (mtmm) REVERT: A 430 MET cc_start: 0.6760 (mtp) cc_final: 0.6550 (mtp) REVERT: B 272 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7768 (mtmm) REVERT: B 430 MET cc_start: 0.6764 (mtp) cc_final: 0.6549 (mtp) REVERT: B 432 GLN cc_start: 0.7198 (mt0) cc_final: 0.6732 (tp40) REVERT: B 674 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7516 (mp) REVERT: B 769 ARG cc_start: 0.7524 (mtt-85) cc_final: 0.7123 (mtp85) outliers start: 38 outliers final: 28 residues processed: 150 average time/residue: 1.0184 time to fit residues: 169.8705 Evaluate side-chains 149 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.183597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115700 restraints weight = 13604.839| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.29 r_work: 0.3257 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14100 Z= 0.171 Angle : 0.574 7.397 19704 Z= 0.285 Chirality : 0.040 0.261 2410 Planarity : 0.004 0.065 1946 Dihedral : 21.031 174.096 4126 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.82 % Allowed : 23.29 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.22 (0.24), residues: 1308 helix: 2.27 (0.22), residues: 512 sheet: 2.00 (0.32), residues: 264 loop : -1.40 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.003 0.001 HIS B 540 PHE 0.014 0.001 PHE A 103 TYR 0.021 0.001 TYR B 650 ARG 0.002 0.000 ARG B 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4487.33 seconds wall clock time: 79 minutes 41.62 seconds (4781.62 seconds total)