Starting phenix.real_space_refine on Thu Nov 20 06:47:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jl3_22371/11_2025/7jl3_22371.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jl3_22371/11_2025/7jl3_22371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jl3_22371/11_2025/7jl3_22371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jl3_22371/11_2025/7jl3_22371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jl3_22371/11_2025/7jl3_22371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jl3_22371/11_2025/7jl3_22371.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12144 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 3 6.06 5 Al 3 5.89 5 P 90 5.49 5 Mg 3 5.21 5 S 120 5.16 5 C 13251 2.51 5 N 3633 2.21 5 O 4104 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21219 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5145 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 624} Chain breaks: 7 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1299 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5145 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 624} Chain breaks: 7 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1299 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5145 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 624} Chain breaks: 7 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "F" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1299 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "X" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 900 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 23, 'rna3p_pyr': 18} Link IDs: {'rna2p': 1, 'rna3p': 40} Chain: "Y" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 885 Classifications: {'RNA': 42} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 24} Link IDs: {'rna3p': 41} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4323 SG CYS A 810 96.252 96.843 76.846 1.00136.66 S ATOM 4349 SG CYS A 813 99.463 98.927 77.236 1.00133.12 S ATOM 4693 SG CYS A 864 98.588 97.784 73.898 1.00142.99 S ATOM 4732 SG CYS A 869 99.736 95.267 76.581 1.00150.16 S ATOM 10767 SG CYS C 810 95.090 66.122 30.617 1.00134.83 S ATOM 10793 SG CYS C 813 97.879 63.500 31.014 1.00134.18 S ATOM 11137 SG CYS C 864 96.564 64.072 27.674 1.00153.89 S ATOM 11176 SG CYS C 869 94.390 62.362 30.359 1.00148.92 S ATOM 17211 SG CYS E 810 66.936 105.513 123.134 1.00135.45 S ATOM 17237 SG CYS E 813 65.696 109.134 123.531 1.00139.28 S ATOM 17581 SG CYS E 864 66.583 108.011 120.190 1.00148.20 S ATOM 17620 SG CYS E 869 69.311 108.510 122.868 1.00148.98 S Time building chain proxies: 5.44, per 1000 atoms: 0.26 Number of scatterers: 21219 At special positions: 0 Unit cell: (161.515, 131.296, 160.473, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 3 29.99 S 120 16.00 P 90 15.00 Al 3 13.00 Mg 3 11.99 F 12 9.00 O 4104 8.00 N 3633 7.00 C 13251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 932.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 813 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 864 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 869 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 810 " pdb=" ZN C2004 " pdb="ZN ZN C2004 " - pdb=" SG CYS C 813 " pdb="ZN ZN C2004 " - pdb=" SG CYS C 864 " pdb="ZN ZN C2004 " - pdb=" SG CYS C 869 " pdb="ZN ZN C2004 " - pdb=" SG CYS C 810 " pdb=" ZN E2004 " pdb="ZN ZN E2004 " - pdb=" SG CYS E 813 " pdb="ZN ZN E2004 " - pdb=" SG CYS E 864 " pdb="ZN ZN E2004 " - pdb=" SG CYS E 869 " pdb="ZN ZN E2004 " - pdb=" SG CYS E 810 " Number of angles added : 18 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 41.6% alpha, 15.4% beta 32 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 244 through 257 removed outlier: 3.507A pdb=" N LEU A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.788A pdb=" N ILE A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.954A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.610A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.527A pdb=" N ASN A 376 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 396 removed outlier: 3.652A pdb=" N GLY A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.517A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.543A pdb=" N GLN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 490 removed outlier: 3.646A pdb=" N ILE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 529 through 558 Processing helix chain 'A' and resid 559 through 574 removed outlier: 4.075A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 602 removed outlier: 3.744A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.673A pdb=" N PHE A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 701 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 744 through 770 removed outlier: 3.808A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 795 removed outlier: 3.854A pdb=" N GLU A 795 " --> pdb=" O ARG A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 841 removed outlier: 3.518A pdb=" N CYS A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 257 removed outlier: 3.507A pdb=" N LEU C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) Proline residue: C 253 - end of helix Processing helix chain 'C' and resid 269 through 284 Processing helix chain 'C' and resid 299 through 314 Processing helix chain 'C' and resid 333 through 341 removed outlier: 3.788A pdb=" N ILE C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 358 removed outlier: 3.955A pdb=" N LEU C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.610A pdb=" N ILE C 365 " --> pdb=" O SER C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 377 removed outlier: 3.527A pdb=" N ASN C 376 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 396 removed outlier: 3.653A pdb=" N GLY C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 434 removed outlier: 3.517A pdb=" N LEU C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.543A pdb=" N GLN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 490 removed outlier: 3.646A pdb=" N ILE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 529 through 558 Processing helix chain 'C' and resid 559 through 574 removed outlier: 4.075A pdb=" N ALA C 563 " --> pdb=" O ARG C 559 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C 564 " --> pdb=" O MET C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 602 removed outlier: 3.745A pdb=" N LYS C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 607 Processing helix chain 'C' and resid 608 through 625 Processing helix chain 'C' and resid 636 through 649 Processing helix chain 'C' and resid 674 through 685 removed outlier: 3.672A pdb=" N PHE C 685 " --> pdb=" O ILE C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 701 Processing helix chain 'C' and resid 720 through 729 Processing helix chain 'C' and resid 744 through 770 removed outlier: 3.807A pdb=" N ILE C 748 " --> pdb=" O ASN C 744 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 766 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 795 removed outlier: 3.854A pdb=" N GLU C 795 " --> pdb=" O ARG C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 841 removed outlier: 3.517A pdb=" N CYS C 841 " --> pdb=" O ALA C 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 257 removed outlier: 3.507A pdb=" N LEU E 248 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Proline residue: E 253 - end of helix Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 299 through 314 Processing helix chain 'E' and resid 333 through 341 removed outlier: 3.788A pdb=" N ILE E 337 " --> pdb=" O PRO E 333 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU E 339 " --> pdb=" O GLU E 335 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.954A pdb=" N LEU E 351 " --> pdb=" O THR E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 366 removed outlier: 3.610A pdb=" N ILE E 365 " --> pdb=" O SER E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 377 removed outlier: 3.528A pdb=" N ASN E 376 " --> pdb=" O GLU E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 396 removed outlier: 3.653A pdb=" N GLY E 396 " --> pdb=" O ASP E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 434 removed outlier: 3.518A pdb=" N LEU E 434 " --> pdb=" O LEU E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 453 removed outlier: 3.543A pdb=" N GLN E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 490 removed outlier: 3.647A pdb=" N ILE E 489 " --> pdb=" O LEU E 485 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS E 490 " --> pdb=" O ALA E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 521 Processing helix chain 'E' and resid 529 through 558 Processing helix chain 'E' and resid 559 through 574 removed outlier: 4.075A pdb=" N ALA E 563 " --> pdb=" O ARG E 559 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU E 564 " --> pdb=" O MET E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 602 removed outlier: 3.745A pdb=" N LYS E 593 " --> pdb=" O ARG E 589 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN E 595 " --> pdb=" O GLU E 591 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU E 596 " --> pdb=" O GLU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 607 Processing helix chain 'E' and resid 608 through 625 Processing helix chain 'E' and resid 636 through 649 Processing helix chain 'E' and resid 674 through 685 removed outlier: 3.673A pdb=" N PHE E 685 " --> pdb=" O ILE E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 701 Processing helix chain 'E' and resid 720 through 729 Processing helix chain 'E' and resid 744 through 770 removed outlier: 3.806A pdb=" N ILE E 748 " --> pdb=" O ASN E 744 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 766 " --> pdb=" O ASN E 762 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 770 " --> pdb=" O LEU E 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 775 through 795 removed outlier: 3.853A pdb=" N GLU E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 841 removed outlier: 3.517A pdb=" N CYS E 841 " --> pdb=" O ALA E 837 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 323 removed outlier: 6.870A pdb=" N THR A 322 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 293 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N MET A 369 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 removed outlier: 6.547A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE A 459 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N THR A 742 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ARG A 461 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY A 659 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 removed outlier: 6.870A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 894 " --> pdb=" O THR A 903 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 823 through 826 Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 844 Processing sheet with id=AA6, first strand: chain 'A' and resid 874 through 878 Processing sheet with id=AA7, first strand: chain 'B' and resid 272 through 274 removed outlier: 4.352A pdb=" N GLU B 316 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B 375 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 387 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU B 401 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE B 389 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 303 removed outlier: 4.209A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS B 348 " --> pdb=" O TRP B 360 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 356 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 357 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 321 through 323 removed outlier: 6.871A pdb=" N THR C 322 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL C 293 " --> pdb=" O ILE C 344 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL C 294 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N MET C 369 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU C 408 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE C 371 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 457 through 462 removed outlier: 6.547A pdb=" N GLN C 457 " --> pdb=" O CYS C 738 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU C 740 " --> pdb=" O GLN C 457 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE C 459 " --> pdb=" O LEU C 740 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N THR C 742 " --> pdb=" O PHE C 459 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ARG C 461 " --> pdb=" O THR C 742 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY C 659 " --> pdb=" O ILE C 695 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 816 through 819 removed outlier: 6.869A pdb=" N LEU C 816 " --> pdb=" O CYS C 810 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N CYS C 810 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 894 " --> pdb=" O THR C 903 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 823 through 826 Processing sheet with id=AB4, first strand: chain 'C' and resid 842 through 844 Processing sheet with id=AB5, first strand: chain 'C' and resid 874 through 878 Processing sheet with id=AB6, first strand: chain 'D' and resid 272 through 274 removed outlier: 4.352A pdb=" N GLU D 316 " --> pdb=" O LYS D 428 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL D 375 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 387 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU D 401 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE D 389 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.209A pdb=" N TRP D 325 " --> pdb=" O TRP D 351 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS D 348 " --> pdb=" O TRP D 360 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 356 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 357 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 321 through 323 removed outlier: 6.871A pdb=" N THR E 322 " --> pdb=" O ILE E 345 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL E 293 " --> pdb=" O ILE E 344 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL E 294 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N MET E 369 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU E 408 " --> pdb=" O MET E 369 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE E 371 " --> pdb=" O LEU E 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 457 through 462 removed outlier: 6.548A pdb=" N GLN E 457 " --> pdb=" O CYS E 738 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU E 740 " --> pdb=" O GLN E 457 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE E 459 " --> pdb=" O LEU E 740 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N THR E 742 " --> pdb=" O PHE E 459 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ARG E 461 " --> pdb=" O THR E 742 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY E 659 " --> pdb=" O ILE E 695 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 816 through 819 removed outlier: 6.869A pdb=" N LEU E 816 " --> pdb=" O CYS E 810 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N CYS E 810 " --> pdb=" O LEU E 816 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL E 894 " --> pdb=" O THR E 903 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 823 through 826 Processing sheet with id=AC3, first strand: chain 'E' and resid 842 through 844 Processing sheet with id=AC4, first strand: chain 'E' and resid 874 through 878 Processing sheet with id=AC5, first strand: chain 'F' and resid 272 through 274 removed outlier: 4.352A pdb=" N GLU F 316 " --> pdb=" O LYS F 428 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL F 375 " --> pdb=" O VAL F 392 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU F 387 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU F 401 " --> pdb=" O LEU F 387 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE F 389 " --> pdb=" O LEU F 399 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 301 through 303 removed outlier: 4.209A pdb=" N TRP F 325 " --> pdb=" O TRP F 351 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS F 348 " --> pdb=" O TRP F 360 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN F 356 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU F 357 " --> pdb=" O LEU F 368 " (cutoff:3.500A) 897 hydrogen bonds defined for protein. 2583 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6169 1.34 - 1.45: 3796 1.45 - 1.57: 11509 1.57 - 1.69: 178 1.69 - 1.81: 174 Bond restraints: 21826 Sorted by residual: bond pdb=" CA LEU E 493 " pdb=" C LEU E 493 " ideal model delta sigma weight residual 1.523 1.623 -0.100 1.34e-02 5.57e+03 5.58e+01 bond pdb=" F2 ALF E2002 " pdb="AL ALF E2002 " ideal model delta sigma weight residual 1.685 1.805 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" F2 ALF C2002 " pdb="AL ALF C2002 " ideal model delta sigma weight residual 1.685 1.805 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.685 1.805 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CA LEU C 493 " pdb=" C LEU C 493 " ideal model delta sigma weight residual 1.520 1.596 -0.076 1.37e-02 5.33e+03 3.05e+01 ... (remaining 21821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.99: 29912 13.99 - 27.98: 14 27.98 - 41.97: 0 41.97 - 55.96: 0 55.96 - 69.95: 6 Bond angle restraints: 29932 Sorted by residual: angle pdb=" F3 ALF C2002 " pdb="AL ALF C2002 " pdb=" F4 ALF C2002 " ideal model delta sigma weight residual 109.63 179.58 -69.95 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F3 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 109.63 179.58 -69.95 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F3 ALF E2002 " pdb="AL ALF E2002 " pdb=" F4 ALF E2002 " ideal model delta sigma weight residual 109.63 179.57 -69.94 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " pdb=" F2 ALF A2002 " ideal model delta sigma weight residual 108.68 178.43 -69.75 3.00e+00 1.11e-01 5.41e+02 angle pdb=" F1 ALF C2002 " pdb="AL ALF C2002 " pdb=" F2 ALF C2002 " ideal model delta sigma weight residual 108.68 178.41 -69.73 3.00e+00 1.11e-01 5.40e+02 ... (remaining 29927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 12620 32.54 - 65.08: 517 65.08 - 97.61: 44 97.61 - 130.15: 3 130.15 - 162.69: 10 Dihedral angle restraints: 13194 sinusoidal: 6015 harmonic: 7179 Sorted by residual: dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 91.72 -151.72 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" C5' ADP C2001 " pdb=" O5' ADP C2001 " pdb=" PA ADP C2001 " pdb=" O2A ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 91.71 -151.71 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" C5' ADP E2001 " pdb=" O5' ADP E2001 " pdb=" PA ADP E2001 " pdb=" O2A ADP E2001 " ideal model delta sinusoidal sigma weight residual -60.00 91.69 -151.69 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 13191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3092 0.071 - 0.143: 339 0.143 - 0.214: 27 0.214 - 0.286: 3 0.286 - 0.357: 1 Chirality restraints: 3462 Sorted by residual: chirality pdb=" CA ASP E 492 " pdb=" N ASP E 492 " pdb=" C ASP E 492 " pdb=" CB ASP E 492 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASP C 492 " pdb=" N ASP C 492 " pdb=" C ASP C 492 " pdb=" CB ASP C 492 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' A X 2 " pdb=" C4' A X 2 " pdb=" O3' A X 2 " pdb=" C2' A X 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 3459 not shown) Planarity restraints: 3435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A X 2 " 0.039 2.00e-02 2.50e+03 1.79e-02 8.82e+00 pdb=" N9 A X 2 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A X 2 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A X 2 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A X 2 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A X 2 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A X 2 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A X 2 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A X 2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A X 2 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A X 2 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 408 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO D 409 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 409 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 409 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 408 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO F 409 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 409 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 409 " -0.037 5.00e-02 4.00e+02 ... (remaining 3432 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 232 2.58 - 3.16: 17853 3.16 - 3.74: 33745 3.74 - 4.32: 43608 4.32 - 4.90: 70310 Nonbonded interactions: 165748 Sorted by model distance: nonbonded pdb=" O1B ADP C2001 " pdb="MG MG C2003 " model vdw 1.999 2.170 nonbonded pdb=" O1B ADP E2001 " pdb="MG MG E2003 " model vdw 2.000 2.170 nonbonded pdb=" O1B ADP A2001 " pdb="MG MG A2003 " model vdw 2.000 2.170 nonbonded pdb=" F4 ALF C2002 " pdb="MG MG C2003 " model vdw 2.015 2.120 nonbonded pdb=" F4 ALF A2002 " pdb="MG MG A2003 " model vdw 2.016 2.120 ... (remaining 165743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.100 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 0.120 21838 Z= 0.217 Angle : 1.318 69.949 29950 Z= 0.553 Chirality : 0.045 0.357 3462 Planarity : 0.004 0.067 3435 Dihedral : 17.306 162.689 8514 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.45 % Allowed : 0.39 % Favored : 98.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2379 helix: 1.47 (0.17), residues: 909 sheet: -0.42 (0.25), residues: 411 loop : -0.45 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 342 TYR 0.035 0.002 TYR E 756 PHE 0.010 0.001 PHE B 389 TRP 0.019 0.001 TRP E 512 HIS 0.011 0.001 HIS C 444 Details of bonding type rmsd covalent geometry : bond 0.00423 (21826) covalent geometry : angle 1.31578 (29932) hydrogen bonds : bond 0.12502 ( 979) hydrogen bonds : angle 5.73676 ( 2747) metal coordination : bond 0.00577 ( 12) metal coordination : angle 3.46759 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 TRP cc_start: 0.8752 (m-90) cc_final: 0.8430 (m-90) REVERT: B 352 LYS cc_start: 0.8964 (ptmt) cc_final: 0.8585 (pttm) REVERT: B 381 ASN cc_start: 0.7676 (p0) cc_final: 0.5907 (p0) REVERT: B 428 LYS cc_start: 0.9068 (tptt) cc_final: 0.8712 (tptp) REVERT: D 352 LYS cc_start: 0.8921 (ptmt) cc_final: 0.8593 (pttm) REVERT: D 417 TYR cc_start: 0.8565 (t80) cc_final: 0.8193 (t80) REVERT: D 428 LYS cc_start: 0.9077 (tptt) cc_final: 0.8714 (tptp) REVERT: E 881 THR cc_start: 0.7416 (t) cc_final: 0.7190 (p) REVERT: F 352 LYS cc_start: 0.9022 (ptmt) cc_final: 0.8650 (pttm) REVERT: F 381 ASN cc_start: 0.7690 (p0) cc_final: 0.6164 (p0) REVERT: F 414 PHE cc_start: 0.8946 (m-10) cc_final: 0.8659 (m-10) REVERT: F 428 LYS cc_start: 0.9099 (tptt) cc_final: 0.8840 (tptp) outliers start: 30 outliers final: 5 residues processed: 321 average time/residue: 0.1621 time to fit residues: 80.2507 Evaluate side-chains 169 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 40.0000 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 623 HIS A 784 GLN B 260 HIS C 623 HIS C 784 GLN D 260 HIS E 404 GLN E 623 HIS E 784 GLN ** F 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.037715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.024739 restraints weight = 167296.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.026095 restraints weight = 83469.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.026999 restraints weight = 52422.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.027553 restraints weight = 38291.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.027909 restraints weight = 31225.135| |-----------------------------------------------------------------------------| r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 21838 Z= 0.295 Angle : 1.025 32.577 29950 Z= 0.459 Chirality : 0.044 0.209 3462 Planarity : 0.005 0.043 3435 Dihedral : 16.982 165.447 3927 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.24 % Allowed : 5.59 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2379 helix: 1.11 (0.16), residues: 939 sheet: -0.05 (0.27), residues: 384 loop : -0.57 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 811 TYR 0.036 0.003 TYR A 756 PHE 0.022 0.002 PHE B 263 TRP 0.012 0.002 TRP E 512 HIS 0.012 0.002 HIS C 375 Details of bonding type rmsd covalent geometry : bond 0.00581 (21826) covalent geometry : angle 1.02144 (29932) hydrogen bonds : bond 0.05291 ( 979) hydrogen bonds : angle 5.19720 ( 2747) metal coordination : bond 0.01763 ( 12) metal coordination : angle 3.67211 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 185 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9284 (mtm) cc_final: 0.9046 (mtp) REVERT: A 335 GLU cc_start: 0.9325 (pt0) cc_final: 0.8923 (pp20) REVERT: A 368 LEU cc_start: 0.9486 (tp) cc_final: 0.9271 (tp) REVERT: A 369 MET cc_start: 0.8990 (mmp) cc_final: 0.8504 (mmm) REVERT: A 385 MET cc_start: 0.9354 (mtp) cc_final: 0.9029 (mmm) REVERT: A 387 MET cc_start: 0.9505 (mmp) cc_final: 0.8905 (mmt) REVERT: A 680 CYS cc_start: 0.9364 (m) cc_final: 0.8999 (p) REVERT: A 724 MET cc_start: 0.9742 (tmm) cc_final: 0.9513 (tmm) REVERT: A 740 LEU cc_start: 0.9604 (tt) cc_final: 0.9277 (mp) REVERT: A 755 MET cc_start: 0.9385 (mtm) cc_final: 0.9125 (mtp) REVERT: B 337 ASP cc_start: 0.9087 (p0) cc_final: 0.8318 (t70) REVERT: B 420 HIS cc_start: 0.9301 (t-90) cc_final: 0.8950 (t-90) REVERT: B 431 LYS cc_start: 0.9225 (mmmm) cc_final: 0.9017 (mmmm) REVERT: C 680 CYS cc_start: 0.9304 (m) cc_final: 0.9006 (t) REVERT: C 724 MET cc_start: 0.9667 (tmm) cc_final: 0.9438 (tmm) REVERT: C 740 LEU cc_start: 0.9593 (tt) cc_final: 0.9184 (mp) REVERT: C 755 MET cc_start: 0.9213 (mtm) cc_final: 0.9007 (ptp) REVERT: D 263 PHE cc_start: 0.8427 (m-80) cc_final: 0.8177 (m-10) REVERT: D 337 ASP cc_start: 0.9046 (p0) cc_final: 0.8378 (t70) REVERT: D 350 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7228 (tm-30) REVERT: D 360 TRP cc_start: 0.8405 (m100) cc_final: 0.7821 (m100) REVERT: D 414 PHE cc_start: 0.9111 (m-10) cc_final: 0.8896 (m-10) REVERT: D 420 HIS cc_start: 0.9324 (t-90) cc_final: 0.8944 (t-90) REVERT: E 255 MET cc_start: 0.9371 (mtm) cc_final: 0.9137 (mtp) REVERT: E 369 MET cc_start: 0.9008 (mmp) cc_final: 0.8738 (mmm) REVERT: E 631 ILE cc_start: 0.9800 (mt) cc_final: 0.9510 (tp) REVERT: E 632 LEU cc_start: 0.9260 (tp) cc_final: 0.9027 (tp) REVERT: E 724 MET cc_start: 0.9706 (tmm) cc_final: 0.9483 (tmm) REVERT: E 740 LEU cc_start: 0.9652 (tt) cc_final: 0.9118 (mp) REVERT: E 741 LEU cc_start: 0.9732 (tp) cc_final: 0.9186 (pp) REVERT: E 755 MET cc_start: 0.9308 (mtm) cc_final: 0.9059 (ptp) REVERT: F 420 HIS cc_start: 0.9290 (t-90) cc_final: 0.8928 (t-90) outliers start: 5 outliers final: 0 residues processed: 190 average time/residue: 0.1646 time to fit residues: 48.3417 Evaluate side-chains 136 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 213 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 219 optimal weight: 0.0770 chunk 16 optimal weight: 0.1980 chunk 122 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 517 GLN A 524 GLN A 573 ASN A 902 GLN B 423 ASN C 524 GLN C 573 ASN C 623 HIS C 902 GLN E 404 GLN E 524 GLN E 573 ASN E 902 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.040160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.026933 restraints weight = 156273.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.028397 restraints weight = 76880.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.029356 restraints weight = 48073.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.029979 restraints weight = 34902.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030384 restraints weight = 28298.729| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21838 Z= 0.111 Angle : 0.907 29.712 29950 Z= 0.379 Chirality : 0.041 0.208 3462 Planarity : 0.004 0.046 3435 Dihedral : 16.554 165.208 3927 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.14 % Allowed : 3.47 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2379 helix: 2.01 (0.16), residues: 936 sheet: -0.08 (0.25), residues: 420 loop : -0.17 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 767 TYR 0.018 0.001 TYR A 756 PHE 0.017 0.001 PHE F 263 TRP 0.013 0.001 TRP E 512 HIS 0.008 0.001 HIS C 557 Details of bonding type rmsd covalent geometry : bond 0.00231 (21826) covalent geometry : angle 0.90470 (29932) hydrogen bonds : bond 0.04013 ( 979) hydrogen bonds : angle 4.55517 ( 2747) metal coordination : bond 0.00319 ( 12) metal coordination : angle 2.56030 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9271 (mtm) cc_final: 0.9013 (mtp) REVERT: A 335 GLU cc_start: 0.9283 (pt0) cc_final: 0.9020 (pm20) REVERT: A 369 MET cc_start: 0.9050 (mmp) cc_final: 0.8780 (mmm) REVERT: A 385 MET cc_start: 0.9338 (mtp) cc_final: 0.9064 (mmm) REVERT: A 387 MET cc_start: 0.9382 (mmp) cc_final: 0.8671 (mmt) REVERT: A 680 CYS cc_start: 0.9360 (m) cc_final: 0.9010 (p) REVERT: A 724 MET cc_start: 0.9702 (tmm) cc_final: 0.9429 (tmm) REVERT: B 420 HIS cc_start: 0.9336 (t-90) cc_final: 0.9034 (t-90) REVERT: C 560 MET cc_start: 0.7712 (tpp) cc_final: 0.7474 (tpt) REVERT: C 724 MET cc_start: 0.9633 (tmm) cc_final: 0.9389 (tmm) REVERT: D 266 LYS cc_start: 0.8975 (tmtt) cc_final: 0.8752 (tptt) REVERT: D 350 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7402 (tm-30) REVERT: D 360 TRP cc_start: 0.8396 (m100) cc_final: 0.7797 (m100) REVERT: D 414 PHE cc_start: 0.9137 (m-10) cc_final: 0.8921 (m-10) REVERT: D 417 TYR cc_start: 0.8352 (t80) cc_final: 0.7838 (t80) REVERT: D 420 HIS cc_start: 0.9364 (t-90) cc_final: 0.9110 (t-90) REVERT: E 255 MET cc_start: 0.9334 (mtm) cc_final: 0.9071 (mtp) REVERT: E 346 LEU cc_start: 0.9268 (tp) cc_final: 0.9013 (tp) REVERT: E 368 LEU cc_start: 0.9482 (tp) cc_final: 0.9270 (tp) REVERT: E 369 MET cc_start: 0.9033 (mmp) cc_final: 0.8602 (mmm) REVERT: E 387 MET cc_start: 0.9602 (mmm) cc_final: 0.9339 (mmp) REVERT: E 724 MET cc_start: 0.9637 (tmm) cc_final: 0.9416 (tmm) REVERT: E 740 LEU cc_start: 0.9581 (tt) cc_final: 0.9155 (mp) REVERT: E 755 MET cc_start: 0.9208 (mtm) cc_final: 0.8986 (mtp) REVERT: F 288 GLN cc_start: 0.9502 (tp40) cc_final: 0.9296 (tp40) REVERT: F 420 HIS cc_start: 0.9333 (t-90) cc_final: 0.9004 (t-90) outliers start: 3 outliers final: 0 residues processed: 214 average time/residue: 0.1577 time to fit residues: 52.7599 Evaluate side-chains 148 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 173 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS C 623 HIS E 517 GLN E 623 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.025575 restraints weight = 162556.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.026963 restraints weight = 81287.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.027860 restraints weight = 51120.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.028451 restraints weight = 37541.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.028833 restraints weight = 30276.240| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21838 Z= 0.198 Angle : 0.932 29.693 29950 Z= 0.399 Chirality : 0.041 0.209 3462 Planarity : 0.004 0.055 3435 Dihedral : 16.585 166.621 3927 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2379 helix: 1.88 (0.16), residues: 936 sheet: 0.06 (0.27), residues: 384 loop : -0.13 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 546 TYR 0.018 0.002 TYR A 756 PHE 0.015 0.002 PHE D 389 TRP 0.007 0.001 TRP F 325 HIS 0.011 0.001 HIS E 557 Details of bonding type rmsd covalent geometry : bond 0.00395 (21826) covalent geometry : angle 0.92866 (29932) hydrogen bonds : bond 0.04068 ( 979) hydrogen bonds : angle 4.68677 ( 2747) metal coordination : bond 0.01165 ( 12) metal coordination : angle 3.16999 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9335 (mtm) cc_final: 0.9055 (mtp) REVERT: A 368 LEU cc_start: 0.9554 (tp) cc_final: 0.9317 (tp) REVERT: A 369 MET cc_start: 0.9005 (mmp) cc_final: 0.8513 (mmm) REVERT: A 385 MET cc_start: 0.9407 (mtp) cc_final: 0.9069 (mmm) REVERT: A 387 MET cc_start: 0.9397 (mmp) cc_final: 0.8716 (mmt) REVERT: A 724 MET cc_start: 0.9764 (tmm) cc_final: 0.9494 (tmm) REVERT: A 741 LEU cc_start: 0.9488 (tp) cc_final: 0.9022 (pp) REVERT: A 755 MET cc_start: 0.9285 (mtm) cc_final: 0.9065 (mtp) REVERT: B 288 GLN cc_start: 0.9214 (tp40) cc_final: 0.8910 (tp40) REVERT: B 337 ASP cc_start: 0.9172 (p0) cc_final: 0.8450 (t70) REVERT: B 420 HIS cc_start: 0.9342 (t-90) cc_final: 0.9006 (t-90) REVERT: B 428 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8617 (tptp) REVERT: C 385 MET cc_start: 0.9308 (mmp) cc_final: 0.8998 (mmm) REVERT: C 560 MET cc_start: 0.8208 (tpp) cc_final: 0.7821 (tpp) REVERT: C 724 MET cc_start: 0.9671 (tmm) cc_final: 0.9421 (tmm) REVERT: C 741 LEU cc_start: 0.9410 (tp) cc_final: 0.9017 (pp) REVERT: C 776 PHE cc_start: 0.9306 (t80) cc_final: 0.9078 (t80) REVERT: D 263 PHE cc_start: 0.8339 (m-80) cc_final: 0.8105 (m-80) REVERT: D 337 ASP cc_start: 0.9184 (p0) cc_final: 0.8568 (t70) REVERT: D 360 TRP cc_start: 0.8444 (m100) cc_final: 0.7863 (m100) REVERT: D 420 HIS cc_start: 0.9282 (t-90) cc_final: 0.8895 (t-90) REVERT: E 255 MET cc_start: 0.9386 (mtm) cc_final: 0.9098 (mtp) REVERT: E 369 MET cc_start: 0.9111 (mmp) cc_final: 0.8801 (mmm) REVERT: E 385 MET cc_start: 0.9252 (mmp) cc_final: 0.8878 (mmm) REVERT: E 724 MET cc_start: 0.9682 (tmm) cc_final: 0.9459 (tmm) REVERT: E 740 LEU cc_start: 0.9568 (tt) cc_final: 0.9146 (mp) REVERT: E 755 MET cc_start: 0.9335 (mtm) cc_final: 0.9080 (mtp) REVERT: F 420 HIS cc_start: 0.9283 (t-90) cc_final: 0.8909 (t-90) REVERT: F 426 ILE cc_start: 0.9433 (mm) cc_final: 0.9211 (mm) REVERT: F 428 LYS cc_start: 0.8867 (tmtt) cc_final: 0.8500 (tptp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1628 time to fit residues: 46.9642 Evaluate side-chains 138 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 11 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 623 HIS C 298 ASN C 306 GLN C 623 HIS E 306 GLN E 517 GLN E 623 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.039756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.026525 restraints weight = 159449.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.027972 restraints weight = 79190.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.028929 restraints weight = 49641.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.029541 restraints weight = 36117.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.029932 restraints weight = 29130.795| |-----------------------------------------------------------------------------| r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21838 Z= 0.112 Angle : 0.889 29.878 29950 Z= 0.368 Chirality : 0.041 0.195 3462 Planarity : 0.003 0.060 3435 Dihedral : 16.400 163.960 3927 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.14 % Allowed : 1.83 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.18), residues: 2379 helix: 2.12 (0.17), residues: 942 sheet: -0.03 (0.25), residues: 432 loop : 0.10 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 342 TYR 0.017 0.001 TYR D 400 PHE 0.015 0.001 PHE F 263 TRP 0.016 0.001 TRP D 292 HIS 0.006 0.001 HIS F 260 Details of bonding type rmsd covalent geometry : bond 0.00234 (21826) covalent geometry : angle 0.88672 (29932) hydrogen bonds : bond 0.03517 ( 979) hydrogen bonds : angle 4.38538 ( 2747) metal coordination : bond 0.00498 ( 12) metal coordination : angle 2.57381 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9347 (mtm) cc_final: 0.9059 (mtp) REVERT: A 368 LEU cc_start: 0.9560 (tp) cc_final: 0.9316 (tp) REVERT: A 369 MET cc_start: 0.9107 (mmp) cc_final: 0.8605 (mmm) REVERT: A 385 MET cc_start: 0.9394 (mtp) cc_final: 0.9072 (mmm) REVERT: A 387 MET cc_start: 0.9346 (mmp) cc_final: 0.8646 (mmt) REVERT: A 680 CYS cc_start: 0.9333 (m) cc_final: 0.8986 (p) REVERT: A 724 MET cc_start: 0.9762 (tmm) cc_final: 0.9485 (tmm) REVERT: A 741 LEU cc_start: 0.9463 (tp) cc_final: 0.8864 (pp) REVERT: A 755 MET cc_start: 0.9261 (mtm) cc_final: 0.9025 (ptp) REVERT: B 288 GLN cc_start: 0.9202 (tp40) cc_final: 0.8966 (tp40) REVERT: B 420 HIS cc_start: 0.9288 (t-90) cc_final: 0.8948 (t-90) REVERT: C 346 LEU cc_start: 0.9477 (tp) cc_final: 0.9202 (tp) REVERT: C 385 MET cc_start: 0.9303 (mmp) cc_final: 0.8989 (mmm) REVERT: C 560 MET cc_start: 0.8223 (tpp) cc_final: 0.7995 (tpp) REVERT: C 724 MET cc_start: 0.9655 (tmm) cc_final: 0.9429 (tmm) REVERT: C 741 LEU cc_start: 0.9381 (tp) cc_final: 0.8795 (pp) REVERT: C 755 MET cc_start: 0.8793 (ptp) cc_final: 0.8480 (ptp) REVERT: D 263 PHE cc_start: 0.8312 (m-80) cc_final: 0.8042 (m-80) REVERT: D 360 TRP cc_start: 0.8348 (m100) cc_final: 0.7893 (m100) REVERT: D 420 HIS cc_start: 0.9285 (t-90) cc_final: 0.8885 (t-90) REVERT: D 427 ILE cc_start: 0.8328 (pt) cc_final: 0.7698 (pt) REVERT: E 255 MET cc_start: 0.9385 (mtm) cc_final: 0.9071 (mtp) REVERT: E 346 LEU cc_start: 0.9370 (tp) cc_final: 0.9118 (tp) REVERT: E 369 MET cc_start: 0.9159 (mmp) cc_final: 0.8875 (mmm) REVERT: E 385 MET cc_start: 0.9241 (mmp) cc_final: 0.8865 (mmm) REVERT: E 560 MET cc_start: 0.7960 (tpp) cc_final: 0.7737 (tpp) REVERT: E 724 MET cc_start: 0.9658 (tmm) cc_final: 0.9412 (tmm) REVERT: E 740 LEU cc_start: 0.9479 (tt) cc_final: 0.9122 (mp) REVERT: E 755 MET cc_start: 0.9306 (mtm) cc_final: 0.9020 (ptp) REVERT: F 321 ASN cc_start: 0.9554 (m-40) cc_final: 0.9269 (t0) REVERT: F 420 HIS cc_start: 0.9306 (t-90) cc_final: 0.8958 (t-90) REVERT: F 431 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7963 (mmtm) outliers start: 3 outliers final: 0 residues processed: 193 average time/residue: 0.1604 time to fit residues: 48.5555 Evaluate side-chains 141 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 166 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS C 623 HIS D 423 ASN E 517 GLN E 623 HIS F 260 HIS F 423 ASN F 429 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.038816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.025872 restraints weight = 161992.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.027218 restraints weight = 80452.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.028157 restraints weight = 51047.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.028755 restraints weight = 37026.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.029169 restraints weight = 30012.161| |-----------------------------------------------------------------------------| r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21838 Z= 0.158 Angle : 0.901 30.485 29950 Z= 0.379 Chirality : 0.041 0.199 3462 Planarity : 0.004 0.061 3435 Dihedral : 16.411 165.911 3927 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2379 helix: 2.13 (0.16), residues: 936 sheet: 0.07 (0.27), residues: 384 loop : -0.03 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 342 TYR 0.015 0.002 TYR A 756 PHE 0.017 0.001 PHE F 389 TRP 0.030 0.001 TRP F 360 HIS 0.005 0.001 HIS F 260 Details of bonding type rmsd covalent geometry : bond 0.00322 (21826) covalent geometry : angle 0.89908 (29932) hydrogen bonds : bond 0.03643 ( 979) hydrogen bonds : angle 4.44421 ( 2747) metal coordination : bond 0.00959 ( 12) metal coordination : angle 2.78784 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9429 (mtm) cc_final: 0.9133 (mtp) REVERT: A 368 LEU cc_start: 0.9566 (tp) cc_final: 0.9324 (tp) REVERT: A 369 MET cc_start: 0.9117 (mmp) cc_final: 0.8583 (mmm) REVERT: A 385 MET cc_start: 0.9428 (mtp) cc_final: 0.9100 (mmm) REVERT: A 387 MET cc_start: 0.9364 (mmp) cc_final: 0.8664 (mmt) REVERT: A 680 CYS cc_start: 0.9356 (m) cc_final: 0.8977 (p) REVERT: A 724 MET cc_start: 0.9774 (tmm) cc_final: 0.9489 (tmm) REVERT: A 741 LEU cc_start: 0.9410 (tp) cc_final: 0.8723 (pp) REVERT: A 755 MET cc_start: 0.9366 (mtm) cc_final: 0.9099 (mtp) REVERT: B 420 HIS cc_start: 0.9313 (t-90) cc_final: 0.8989 (t-90) REVERT: B 427 ILE cc_start: 0.8594 (pt) cc_final: 0.7983 (pt) REVERT: C 255 MET cc_start: 0.9423 (mtm) cc_final: 0.9221 (mtp) REVERT: C 346 LEU cc_start: 0.9501 (tp) cc_final: 0.9246 (tp) REVERT: C 385 MET cc_start: 0.9319 (mmp) cc_final: 0.9013 (mmm) REVERT: C 724 MET cc_start: 0.9669 (tmm) cc_final: 0.9405 (tmm) REVERT: C 741 LEU cc_start: 0.9279 (tp) cc_final: 0.8660 (pp) REVERT: C 755 MET cc_start: 0.8913 (ptp) cc_final: 0.8603 (ptp) REVERT: D 263 PHE cc_start: 0.8331 (m-80) cc_final: 0.8014 (m-80) REVERT: D 360 TRP cc_start: 0.8385 (m100) cc_final: 0.7939 (m100) REVERT: D 420 HIS cc_start: 0.9219 (t-90) cc_final: 0.8819 (t-90) REVERT: D 427 ILE cc_start: 0.8441 (pt) cc_final: 0.7966 (pt) REVERT: E 255 MET cc_start: 0.9426 (mtm) cc_final: 0.9103 (mtp) REVERT: E 346 LEU cc_start: 0.9386 (tp) cc_final: 0.9147 (tp) REVERT: E 369 MET cc_start: 0.9216 (mmp) cc_final: 0.8851 (mmm) REVERT: E 385 MET cc_start: 0.9255 (mmp) cc_final: 0.8885 (mmm) REVERT: E 387 MET cc_start: 0.9617 (mmm) cc_final: 0.9210 (mmm) REVERT: E 560 MET cc_start: 0.8146 (tpp) cc_final: 0.7901 (tpp) REVERT: E 724 MET cc_start: 0.9674 (tmm) cc_final: 0.9424 (tmm) REVERT: E 740 LEU cc_start: 0.9483 (tt) cc_final: 0.9151 (mp) REVERT: E 755 MET cc_start: 0.9380 (mtm) cc_final: 0.9112 (mtp) REVERT: F 420 HIS cc_start: 0.9320 (t-90) cc_final: 0.8998 (t-90) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1636 time to fit residues: 46.4261 Evaluate side-chains 134 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 25 optimal weight: 0.0040 chunk 170 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS C 623 HIS E 517 GLN E 623 HIS ** F 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.039282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.026156 restraints weight = 160855.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.027594 restraints weight = 80365.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.028544 restraints weight = 50584.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.029147 restraints weight = 36877.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.029539 restraints weight = 29774.957| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21838 Z= 0.126 Angle : 0.887 30.266 29950 Z= 0.369 Chirality : 0.041 0.191 3462 Planarity : 0.003 0.062 3435 Dihedral : 16.294 164.473 3927 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2379 helix: 2.22 (0.17), residues: 942 sheet: 0.10 (0.27), residues: 384 loop : 0.06 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 296 TYR 0.015 0.001 TYR A 756 PHE 0.017 0.001 PHE E 776 TRP 0.013 0.001 TRP B 360 HIS 0.004 0.001 HIS F 260 Details of bonding type rmsd covalent geometry : bond 0.00263 (21826) covalent geometry : angle 0.88461 (29932) hydrogen bonds : bond 0.03409 ( 979) hydrogen bonds : angle 4.34175 ( 2747) metal coordination : bond 0.00688 ( 12) metal coordination : angle 2.61637 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9424 (mtm) cc_final: 0.9121 (mtp) REVERT: A 368 LEU cc_start: 0.9573 (tp) cc_final: 0.9343 (tp) REVERT: A 369 MET cc_start: 0.9136 (mmp) cc_final: 0.8641 (mmm) REVERT: A 385 MET cc_start: 0.9422 (mtp) cc_final: 0.9083 (mmm) REVERT: A 387 MET cc_start: 0.9329 (mmp) cc_final: 0.8633 (mmt) REVERT: A 520 CYS cc_start: 0.9438 (m) cc_final: 0.9227 (m) REVERT: A 680 CYS cc_start: 0.9338 (m) cc_final: 0.8953 (p) REVERT: A 724 MET cc_start: 0.9774 (tmm) cc_final: 0.9401 (tmm) REVERT: A 741 LEU cc_start: 0.9367 (tp) cc_final: 0.8670 (pp) REVERT: A 755 MET cc_start: 0.9376 (mtm) cc_final: 0.9086 (mtp) REVERT: B 288 GLN cc_start: 0.9214 (tp40) cc_final: 0.8975 (tp40) REVERT: B 420 HIS cc_start: 0.9296 (t-90) cc_final: 0.8973 (t-90) REVERT: B 427 ILE cc_start: 0.8533 (pt) cc_final: 0.7887 (pt) REVERT: C 255 MET cc_start: 0.9414 (mtm) cc_final: 0.9188 (mtp) REVERT: C 346 LEU cc_start: 0.9459 (tp) cc_final: 0.9211 (tp) REVERT: C 379 LYS cc_start: 0.9541 (mtmm) cc_final: 0.9250 (pttm) REVERT: C 385 MET cc_start: 0.9292 (mmp) cc_final: 0.8981 (mmm) REVERT: C 724 MET cc_start: 0.9651 (tmm) cc_final: 0.9285 (tmm) REVERT: C 741 LEU cc_start: 0.9240 (tp) cc_final: 0.8594 (pp) REVERT: C 755 MET cc_start: 0.8935 (ptp) cc_final: 0.8647 (ptp) REVERT: D 263 PHE cc_start: 0.8382 (m-80) cc_final: 0.8001 (m-80) REVERT: D 360 TRP cc_start: 0.8370 (m100) cc_final: 0.7956 (m100) REVERT: D 420 HIS cc_start: 0.9148 (t-90) cc_final: 0.8742 (t-90) REVERT: D 426 ILE cc_start: 0.9321 (mp) cc_final: 0.9094 (mp) REVERT: D 427 ILE cc_start: 0.8430 (pt) cc_final: 0.7872 (pt) REVERT: E 255 MET cc_start: 0.9423 (mtm) cc_final: 0.9092 (mtp) REVERT: E 346 LEU cc_start: 0.9384 (tp) cc_final: 0.9159 (tp) REVERT: E 369 MET cc_start: 0.9250 (mmp) cc_final: 0.8881 (mmm) REVERT: E 385 MET cc_start: 0.9243 (mmp) cc_final: 0.8885 (mmm) REVERT: E 520 CYS cc_start: 0.9475 (m) cc_final: 0.9269 (m) REVERT: E 724 MET cc_start: 0.9664 (tmm) cc_final: 0.9431 (tmm) REVERT: E 740 LEU cc_start: 0.9450 (tt) cc_final: 0.9153 (mp) REVERT: E 755 MET cc_start: 0.9376 (mtm) cc_final: 0.9120 (mtp) REVERT: F 321 ASN cc_start: 0.9511 (m-40) cc_final: 0.9197 (t0) REVERT: F 420 HIS cc_start: 0.9310 (t-90) cc_final: 0.8961 (t-90) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1548 time to fit residues: 45.4838 Evaluate side-chains 137 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS C 623 HIS E 517 GLN E 623 HIS ** F 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.038584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.025756 restraints weight = 161936.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.027128 restraints weight = 81200.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.028066 restraints weight = 51178.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.028640 restraints weight = 37248.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.029047 restraints weight = 30325.412| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21838 Z= 0.172 Angle : 0.906 31.112 29950 Z= 0.383 Chirality : 0.041 0.198 3462 Planarity : 0.004 0.062 3435 Dihedral : 16.310 166.106 3927 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 2379 helix: 2.12 (0.16), residues: 936 sheet: 0.08 (0.27), residues: 384 loop : 0.04 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 291 TYR 0.021 0.002 TYR A 622 PHE 0.015 0.001 PHE F 389 TRP 0.011 0.001 TRP F 360 HIS 0.006 0.001 HIS F 260 Details of bonding type rmsd covalent geometry : bond 0.00349 (21826) covalent geometry : angle 0.90296 (29932) hydrogen bonds : bond 0.03598 ( 979) hydrogen bonds : angle 4.44940 ( 2747) metal coordination : bond 0.01027 ( 12) metal coordination : angle 2.99564 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9436 (mtm) cc_final: 0.9122 (mtp) REVERT: A 368 LEU cc_start: 0.9495 (tp) cc_final: 0.9287 (tp) REVERT: A 369 MET cc_start: 0.9160 (mmp) cc_final: 0.8612 (mmm) REVERT: A 385 MET cc_start: 0.9451 (mtp) cc_final: 0.9094 (mmm) REVERT: A 387 MET cc_start: 0.9341 (mmp) cc_final: 0.8637 (mmt) REVERT: A 680 CYS cc_start: 0.9328 (m) cc_final: 0.8891 (p) REVERT: A 724 MET cc_start: 0.9781 (tmm) cc_final: 0.9488 (tmm) REVERT: A 741 LEU cc_start: 0.9346 (tp) cc_final: 0.8624 (pp) REVERT: A 755 MET cc_start: 0.9419 (mtm) cc_final: 0.9088 (mtp) REVERT: B 288 GLN cc_start: 0.9175 (tp40) cc_final: 0.8947 (tp40) REVERT: B 420 HIS cc_start: 0.9234 (t-90) cc_final: 0.8916 (t-90) REVERT: B 427 ILE cc_start: 0.8624 (pt) cc_final: 0.8071 (pt) REVERT: C 255 MET cc_start: 0.9434 (mtm) cc_final: 0.9202 (mtp) REVERT: C 385 MET cc_start: 0.9297 (mmp) cc_final: 0.8973 (mmm) REVERT: C 724 MET cc_start: 0.9653 (tmm) cc_final: 0.9300 (tmm) REVERT: C 741 LEU cc_start: 0.9239 (tp) cc_final: 0.8593 (pp) REVERT: C 776 PHE cc_start: 0.9230 (t80) cc_final: 0.9021 (t80) REVERT: D 263 PHE cc_start: 0.8387 (m-80) cc_final: 0.8028 (m-80) REVERT: D 360 TRP cc_start: 0.8416 (m100) cc_final: 0.7995 (m100) REVERT: D 420 HIS cc_start: 0.9118 (t-90) cc_final: 0.8707 (t-90) REVERT: D 426 ILE cc_start: 0.9338 (mp) cc_final: 0.9013 (mp) REVERT: D 427 ILE cc_start: 0.8435 (pt) cc_final: 0.7838 (pt) REVERT: E 255 MET cc_start: 0.9438 (mtm) cc_final: 0.9098 (mtp) REVERT: E 346 LEU cc_start: 0.9356 (tp) cc_final: 0.9120 (tp) REVERT: E 369 MET cc_start: 0.9271 (mmp) cc_final: 0.8894 (mmm) REVERT: E 385 MET cc_start: 0.9225 (mmp) cc_final: 0.8836 (mmm) REVERT: E 520 CYS cc_start: 0.9457 (m) cc_final: 0.9245 (m) REVERT: E 724 MET cc_start: 0.9667 (tmm) cc_final: 0.9426 (tmm) REVERT: E 740 LEU cc_start: 0.9446 (tt) cc_final: 0.9180 (mp) REVERT: E 755 MET cc_start: 0.9431 (mtm) cc_final: 0.9141 (mtp) REVERT: F 420 HIS cc_start: 0.9255 (t-90) cc_final: 0.8919 (t-90) REVERT: F 426 ILE cc_start: 0.9356 (mm) cc_final: 0.9143 (mm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1585 time to fit residues: 43.6172 Evaluate side-chains 128 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 187 optimal weight: 0.0020 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 0.1980 chunk 159 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 246 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 129 optimal weight: 0.0970 chunk 83 optimal weight: 7.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS C 623 HIS E 341 ASN E 517 GLN E 623 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.040195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.027124 restraints weight = 157799.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.028558 restraints weight = 78693.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.029522 restraints weight = 49946.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.030159 restraints weight = 36297.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.030568 restraints weight = 29263.234| |-----------------------------------------------------------------------------| r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21838 Z= 0.102 Angle : 0.887 29.676 29950 Z= 0.366 Chirality : 0.041 0.183 3462 Planarity : 0.003 0.066 3435 Dihedral : 16.083 162.738 3927 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.18), residues: 2379 helix: 2.32 (0.17), residues: 933 sheet: -0.12 (0.26), residues: 417 loop : 0.18 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 342 TYR 0.025 0.001 TYR D 400 PHE 0.018 0.001 PHE E 776 TRP 0.013 0.001 TRP A 512 HIS 0.004 0.001 HIS E 557 Details of bonding type rmsd covalent geometry : bond 0.00212 (21826) covalent geometry : angle 0.88576 (29932) hydrogen bonds : bond 0.03285 ( 979) hydrogen bonds : angle 4.21100 ( 2747) metal coordination : bond 0.00256 ( 12) metal coordination : angle 2.26188 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9452 (mtm) cc_final: 0.9136 (mtp) REVERT: A 368 LEU cc_start: 0.9552 (tp) cc_final: 0.9213 (tp) REVERT: A 369 MET cc_start: 0.9131 (mmp) cc_final: 0.8474 (mmm) REVERT: A 385 MET cc_start: 0.9406 (mtp) cc_final: 0.9057 (mmm) REVERT: A 387 MET cc_start: 0.9277 (mmp) cc_final: 0.8661 (mmt) REVERT: A 724 MET cc_start: 0.9770 (tmm) cc_final: 0.9338 (tmm) REVERT: A 741 LEU cc_start: 0.9286 (tp) cc_final: 0.8578 (pp) REVERT: A 755 MET cc_start: 0.9362 (mtm) cc_final: 0.9062 (mtp) REVERT: B 288 GLN cc_start: 0.9215 (tp40) cc_final: 0.8961 (tp40) REVERT: B 401 GLU cc_start: 0.9005 (pm20) cc_final: 0.8785 (mp0) REVERT: B 420 HIS cc_start: 0.9303 (t-90) cc_final: 0.9019 (t-90) REVERT: B 427 ILE cc_start: 0.8626 (pt) cc_final: 0.8002 (pt) REVERT: C 255 MET cc_start: 0.9403 (mtm) cc_final: 0.9173 (mtp) REVERT: C 346 LEU cc_start: 0.9469 (tp) cc_final: 0.9246 (tp) REVERT: C 385 MET cc_start: 0.9266 (mmp) cc_final: 0.8966 (mmm) REVERT: C 520 CYS cc_start: 0.9406 (m) cc_final: 0.9119 (m) REVERT: C 521 MET cc_start: 0.9244 (ptp) cc_final: 0.9016 (pmm) REVERT: C 560 MET cc_start: 0.8251 (tpp) cc_final: 0.7764 (tpp) REVERT: C 724 MET cc_start: 0.9634 (tmm) cc_final: 0.9252 (tmm) REVERT: C 741 LEU cc_start: 0.9182 (tp) cc_final: 0.8498 (pp) REVERT: D 263 PHE cc_start: 0.8413 (m-80) cc_final: 0.8038 (m-80) REVERT: D 288 GLN cc_start: 0.9401 (tp40) cc_final: 0.9197 (tp40) REVERT: D 360 TRP cc_start: 0.8588 (m100) cc_final: 0.8062 (m100) REVERT: D 420 HIS cc_start: 0.9165 (t-90) cc_final: 0.8750 (t-90) REVERT: D 427 ILE cc_start: 0.8649 (pt) cc_final: 0.8147 (pt) REVERT: E 255 MET cc_start: 0.9462 (mtm) cc_final: 0.9130 (mtp) REVERT: E 346 LEU cc_start: 0.9402 (tp) cc_final: 0.9170 (tp) REVERT: E 369 MET cc_start: 0.9237 (mmp) cc_final: 0.8929 (mmm) REVERT: E 385 MET cc_start: 0.9247 (mmp) cc_final: 0.8894 (mmm) REVERT: E 520 CYS cc_start: 0.9362 (m) cc_final: 0.9133 (m) REVERT: E 560 MET cc_start: 0.7975 (tpp) cc_final: 0.7725 (tpp) REVERT: E 724 MET cc_start: 0.9627 (tmm) cc_final: 0.9383 (tmm) REVERT: E 755 MET cc_start: 0.9388 (mtm) cc_final: 0.9115 (mtp) REVERT: F 420 HIS cc_start: 0.9345 (t-90) cc_final: 0.9047 (t-90) REVERT: F 426 ILE cc_start: 0.9332 (mm) cc_final: 0.9131 (mm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1581 time to fit residues: 47.9988 Evaluate side-chains 142 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 8 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 147 optimal weight: 0.0060 chunk 217 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS C 623 HIS E 517 GLN E 623 HIS ** F 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.038481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.025668 restraints weight = 164601.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.027041 restraints weight = 82413.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.027977 restraints weight = 52248.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.028572 restraints weight = 38105.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.028969 restraints weight = 30603.164| |-----------------------------------------------------------------------------| r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21838 Z= 0.188 Angle : 0.918 31.171 29950 Z= 0.392 Chirality : 0.041 0.201 3462 Planarity : 0.004 0.063 3435 Dihedral : 16.290 166.505 3927 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 2379 helix: 2.09 (0.17), residues: 939 sheet: -0.08 (0.26), residues: 435 loop : 0.16 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 291 TYR 0.014 0.002 TYR A 756 PHE 0.016 0.002 PHE D 389 TRP 0.014 0.001 TRP B 360 HIS 0.007 0.001 HIS F 260 Details of bonding type rmsd covalent geometry : bond 0.00378 (21826) covalent geometry : angle 0.91551 (29932) hydrogen bonds : bond 0.03637 ( 979) hydrogen bonds : angle 4.47261 ( 2747) metal coordination : bond 0.01140 ( 12) metal coordination : angle 3.03096 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9486 (mtm) cc_final: 0.9169 (mtp) REVERT: A 368 LEU cc_start: 0.9484 (tp) cc_final: 0.9235 (tp) REVERT: A 369 MET cc_start: 0.9195 (mmp) cc_final: 0.8647 (mmm) REVERT: A 385 MET cc_start: 0.9449 (mtp) cc_final: 0.9072 (mmt) REVERT: A 680 CYS cc_start: 0.9270 (m) cc_final: 0.8936 (p) REVERT: A 682 LEU cc_start: 0.9641 (tt) cc_final: 0.9431 (pp) REVERT: A 724 MET cc_start: 0.9778 (tmm) cc_final: 0.9381 (tmm) REVERT: A 741 LEU cc_start: 0.9314 (tp) cc_final: 0.8539 (pp) REVERT: A 755 MET cc_start: 0.9442 (mtm) cc_final: 0.9094 (mtp) REVERT: B 288 GLN cc_start: 0.9131 (tp40) cc_final: 0.8904 (tp40) REVERT: B 420 HIS cc_start: 0.9233 (t-90) cc_final: 0.8915 (t-90) REVERT: B 427 ILE cc_start: 0.8687 (pt) cc_final: 0.8014 (pt) REVERT: C 255 MET cc_start: 0.9455 (mtm) cc_final: 0.9207 (mtp) REVERT: C 385 MET cc_start: 0.9304 (mmp) cc_final: 0.8993 (mmm) REVERT: C 520 CYS cc_start: 0.9425 (m) cc_final: 0.9137 (m) REVERT: C 521 MET cc_start: 0.9309 (ptp) cc_final: 0.9065 (pmm) REVERT: C 724 MET cc_start: 0.9658 (tmm) cc_final: 0.9332 (tmm) REVERT: C 741 LEU cc_start: 0.9215 (tp) cc_final: 0.8536 (pp) REVERT: C 776 PHE cc_start: 0.9236 (t80) cc_final: 0.9020 (t80) REVERT: D 263 PHE cc_start: 0.8388 (m-80) cc_final: 0.7982 (m-80) REVERT: D 297 PHE cc_start: 0.8558 (m-10) cc_final: 0.8228 (m-80) REVERT: D 360 TRP cc_start: 0.8468 (m100) cc_final: 0.8029 (m100) REVERT: D 420 HIS cc_start: 0.9130 (t-90) cc_final: 0.8695 (t-90) REVERT: D 426 ILE cc_start: 0.9333 (mp) cc_final: 0.9050 (mp) REVERT: D 427 ILE cc_start: 0.8736 (pt) cc_final: 0.8241 (pt) REVERT: E 255 MET cc_start: 0.9478 (mtm) cc_final: 0.9123 (mtp) REVERT: E 346 LEU cc_start: 0.9362 (tp) cc_final: 0.9112 (tp) REVERT: E 369 MET cc_start: 0.9260 (mmp) cc_final: 0.8823 (mmm) REVERT: E 385 MET cc_start: 0.9258 (mmp) cc_final: 0.8844 (mmm) REVERT: E 387 MET cc_start: 0.9613 (mmm) cc_final: 0.9276 (mmm) REVERT: E 520 CYS cc_start: 0.9403 (m) cc_final: 0.9182 (m) REVERT: E 724 MET cc_start: 0.9663 (tmm) cc_final: 0.9408 (tmm) REVERT: E 755 MET cc_start: 0.9470 (mtm) cc_final: 0.9150 (mtp) REVERT: F 420 HIS cc_start: 0.9287 (t-90) cc_final: 0.8962 (t-90) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1524 time to fit residues: 43.0216 Evaluate side-chains 136 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 177 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 87 optimal weight: 0.2980 chunk 194 optimal weight: 10.0000 chunk 213 optimal weight: 0.2980 chunk 126 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS C 623 HIS E 517 GLN E 623 HIS ** F 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.025466 restraints weight = 164383.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.026834 restraints weight = 82171.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.027758 restraints weight = 51807.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.028339 restraints weight = 37779.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.028717 restraints weight = 30442.408| |-----------------------------------------------------------------------------| r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21838 Z= 0.196 Angle : 0.930 30.803 29950 Z= 0.400 Chirality : 0.042 0.194 3462 Planarity : 0.004 0.061 3435 Dihedral : 16.446 165.950 3927 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2379 helix: 1.91 (0.16), residues: 939 sheet: -0.15 (0.26), residues: 396 loop : 0.03 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 732 TYR 0.015 0.002 TYR A 756 PHE 0.020 0.002 PHE C 314 TRP 0.015 0.002 TRP B 360 HIS 0.008 0.001 HIS F 260 Details of bonding type rmsd covalent geometry : bond 0.00396 (21826) covalent geometry : angle 0.92654 (29932) hydrogen bonds : bond 0.03739 ( 979) hydrogen bonds : angle 4.56160 ( 2747) metal coordination : bond 0.01316 ( 12) metal coordination : angle 3.38285 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.42 seconds wall clock time: 65 minutes 16.89 seconds (3916.89 seconds total)