Starting phenix.real_space_refine on Thu Oct 29 05:36:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jl3_22371/10_2026/7jl3_22371.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jl3_22371/10_2026/7jl3_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_22371/10_2026/7jl3_22371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jl3_22371/10_2026/7jl3_22371.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jl3_22371/10_2026/7jl3_22371.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jl3_22371/10_2026/7jl3_22371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jl3_22371/10_2026/7jl3_22371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jl3_22371/10_2026/7jl3_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 4.10, per 1000 atoms: 0.19 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: 1.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.51 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: 4.47 Time building geometry restraints manager: 2.47 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: 12430 32.54 - 65.08: 430 65.08 - 97.61: 27 97.61 - 130.15: 3 130.15 - 162.69: 10 Dihedral angle restraints: 12900 sinusoidal: 5721 harmonic: 7179 Sorted by residual: dihedral pdb=" C4' A X 2 " pdb=" C3' A X 2 " pdb=" C2' A X 2 " pdb=" C1' A X 2 " ideal model delta sinusoidal sigma weight residual 36.34 -34.17 70.52 1 3.10e+00 1.04e-01 6.66e+02 dihedral pdb=" O4' A X 2 " pdb=" C4' A X 2 " pdb=" C3' A X 2 " pdb=" C2' A X 2 " ideal model delta sinusoidal sigma weight residual -35.15 22.06 -57.21 1 4.00e+00 6.25e-02 2.75e+02 dihedral pdb=" O4' A X 2 " pdb=" C2' A X 2 " pdb=" C1' A X 2 " pdb=" C3' A X 2 " ideal model delta sinusoidal sigma weight residual -94.41 -35.50 -58.90 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 12897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3095 0.080 - 0.160: 266 0.160 - 0.240: 81 0.240 - 0.320: 18 0.320 - 0.400: 2 Chirality restraints: 3462 Sorted by residual: chirality pdb=" C2' A X 2 " pdb=" C3' A X 2 " pdb=" O2' A X 2 " pdb=" C1' A X 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.39 -0.40 2.00e-01 2.50e+01 4.00e+00 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=" P C X 3 " pdb=" OP1 C X 3 " pdb=" OP2 C X 3 " pdb=" O5' C X 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.22e+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: 2.360 Set stop_for_unknowns flag: 0.010 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.430 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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= 0.219 Angle : 1.337 69.949 29950 Z= 0.554 Chirality : 0.058 0.400 3462 Planarity : 0.004 0.067 3435 Dihedral : 16.261 162.689 8220 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/Z covalent geometry : bond 0.00429 / 0.22 (21826) covalent geometry : angle 1.33473 / 0.55 (29932) hydrogen bonds : bond 0.12502 / 8.04 ( 979) hydrogen bonds : angle 5.73676 / 4.06 ( 2747) metal coordination : bond 0.00577 / 0.34 ( 12) metal coordination : angle 3.46759 / 2.08 ( 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 : 0.815 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: 0.7675 (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: 0.9078 (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: 0.1473 time to fit residues: 73.8180 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 : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] 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: 6.9990 chunk 66 optimal weight: 40.0000 chunk 247 optimal weight: 7.9990 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... 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 = 0.2857 r_free = 0.2857 target = 0.037801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.024867 restraints weight = 168278.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.026221 restraints weight = 83558.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.027125 restraints weight = 52304.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.027684 restraints weight = 38275.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.028049 restraints weight = 31179.993| |-----------------------------------------------------------------------------| r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 21838 Z= 0.296 Angle : 1.090 32.618 29950 Z= 0.467 Chirality : 0.049 0.363 3462 Planarity : 0.005 0.044 3435 Dihedral : 14.088 178.908 3633 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.24 % Allowed : 5.39 % Favored : 94.36 % 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: 0.30 (0.17), residues: 2379 helix: 1.17 (0.16), residues: 939 sheet: -0.22 (0.26), residues: 414 loop : -0.44 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 811 TYR 0.035 0.002 TYR A 756 PHE 0.023 0.002 PHE B 263 TRP 0.012 0.002 TRP E 512 HIS 0.011 0.002 HIS C 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.30 (21826) covalent geometry : angle 1.08641 / 0.47 (29932) hydrogen bonds : bond 0.05291 / 3.57 ( 979) hydrogen bonds : angle 5.18902 / 3.69 ( 2747) metal coordination : bond 0.01729 / 1.08 ( 12) metal coordination : angle 3.62004 / 2.52 ( 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 191 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 186 time to evaluate : 0.585 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: 0.9276 (mtm) cc_final: 0.9028 (mtp) REVERT: A 335 GLU cc_start: 0.9324 (pt0) cc_final: 0.8922 (pp20) REVERT: A 368 LEU cc_start: 0.9482 (tp) cc_final: 0.9255 (tp) REVERT: A 369 MET cc_start: 0.8967 (mmp) cc_final: 0.8487 (mmm) REVERT: A 385 MET cc_start: 0.9371 (mtp) cc_final: 0.9051 (mmm) REVERT: A 387 MET cc_start: 0.9514 (mmp) cc_final: 0.8912 (mmt) REVERT: A 680 CYS cc_start: 0.9368 (m) cc_final: 0.9005 (p) REVERT: A 724 MET cc_start: 0.9745 (tmm) cc_final: 0.9511 (tmm) REVERT: A 740 LEU cc_start: 0.9614 (tt) cc_final: 0.9271 (mp) REVERT: A 755 MET cc_start: 0.9373 (mtm) cc_final: 0.9108 (mtp) REVERT: B 337 ASP cc_start: 0.9085 (p0) cc_final: 0.8333 (t70) REVERT: B 420 HIS cc_start: 0.9309 (t-90) cc_final: 0.8954 (t-90) REVERT: B 431 LYS cc_start: 0.9223 (mmmm) cc_final: 0.9020 (mmmm) REVERT: C 680 CYS cc_start: 0.9305 (m) cc_final: 0.9007 (t) REVERT: C 724 MET cc_start: 0.9666 (tmm) cc_final: 0.9439 (tmm) REVERT: C 740 LEU cc_start: 0.9598 (tt) cc_final: 0.9190 (mp) REVERT: C 755 MET cc_start: 0.9204 (mtm) cc_final: 0.9003 (ptp) REVERT: D 263 PHE cc_start: 0.8446 (m-80) cc_final: 0.8190 (m-10) REVERT: D 337 ASP cc_start: 0.9043 (p0) cc_final: 0.8376 (t70) REVERT: D 350 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7118 (tm-30) REVERT: D 360 TRP cc_start: 0.8410 (m100) cc_final: 0.7863 (m100) REVERT: D 414 PHE cc_start: 0.9098 (m-10) cc_final: 0.8871 (m-10) REVERT: D 420 HIS cc_start: 0.9327 (t-90) cc_final: 0.8946 (t-90) REVERT: E 255 MET cc_start: 0.9364 (mtm) cc_final: 0.9118 (mtp) REVERT: E 369 MET cc_start: 0.9004 (mmp) cc_final: 0.8751 (mmm) REVERT: E 631 ILE cc_start: 0.9795 (mt) cc_final: 0.9527 (tp) REVERT: E 632 LEU cc_start: 0.9271 (tp) cc_final: 0.9023 (tp) REVERT: E 724 MET cc_start: 0.9691 (tmm) cc_final: 0.9476 (tmm) REVERT: E 740 LEU cc_start: 0.9648 (tt) cc_final: 0.9110 (mp) REVERT: E 741 LEU cc_start: 0.9743 (tp) cc_final: 0.9207 (pp) REVERT: E 755 MET cc_start: 0.9303 (mtm) cc_final: 0.9053 (ptp) REVERT: F 420 HIS cc_start: 0.9300 (t-90) cc_final: 0.8933 (t-90) outliers start: 5 outliers final: 0 residues processed: 191 average time/residue: 0.1524 time to fit residues: 45.4240 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 : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [213, 120, 219, 16, 122, 82, 215, 62, 144, 94, 206] chunk 213 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 219 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 524 GLN E 573 ASN E 902 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.039646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.026402 restraints weight = 157989.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.027839 restraints weight = 77746.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.028779 restraints weight = 48926.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.029429 restraints weight = 35690.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.029818 restraints weight = 28609.320| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21838 Z= 0.126 Angle : 0.951 29.538 29950 Z= 0.389 Chirality : 0.046 0.345 3462 Planarity : 0.004 0.045 3435 Dihedral : 13.307 168.464 3633 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.01 % 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: 0.93 (0.17), residues: 2379 helix: 1.90 (0.16), residues: 936 sheet: -0.11 (0.25), residues: 414 loop : -0.19 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 291 TYR 0.020 0.002 TYR A 756 PHE 0.018 0.001 PHE B 263 TRP 0.013 0.001 TRP A 512 HIS 0.010 0.001 HIS C 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (21826) covalent geometry : angle 0.94887 / 0.39 (29932) hydrogen bonds : bond 0.04145 / 2.80 ( 979) hydrogen bonds : angle 4.63960 / 3.30 ( 2747) metal coordination : bond 0.00475 / 0.29 ( 12) metal coordination : angle 2.70221 / 1.83 ( 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 208 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 205 time to evaluate : 0.830 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: A 255 MET cc_start: 0.9275 (mtm) cc_final: 0.9018 (mtp) REVERT: A 335 GLU cc_start: 0.9284 (pt0) cc_final: 0.8798 (pp20) REVERT: A 368 LEU cc_start: 0.9509 (tp) cc_final: 0.9306 (tp) REVERT: A 369 MET cc_start: 0.9054 (mmp) cc_final: 0.8802 (mmm) REVERT: A 385 MET cc_start: 0.9342 (mtp) cc_final: 0.9062 (mmm) REVERT: A 387 MET cc_start: 0.9390 (mmp) cc_final: 0.8692 (mmt) REVERT: A 680 CYS cc_start: 0.9357 (m) cc_final: 0.8966 (p) REVERT: A 724 MET cc_start: 0.9715 (tmm) cc_final: 0.9448 (tmm) REVERT: A 755 MET cc_start: 0.9271 (mtm) cc_final: 0.9034 (mtp) REVERT: B 420 HIS cc_start: 0.9328 (t-90) cc_final: 0.9022 (t-90) REVERT: B 424 TYR cc_start: 0.9104 (p90) cc_final: 0.8901 (p90) REVERT: B 431 LYS cc_start: 0.9268 (mmmm) cc_final: 0.9005 (mmmm) REVERT: C 724 MET cc_start: 0.9649 (tmm) cc_final: 0.9393 (tmm) REVERT: D 263 PHE cc_start: 0.8322 (m-80) cc_final: 0.8121 (m-80) REVERT: D 350 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7341 (tm-30) REVERT: D 360 TRP cc_start: 0.8418 (m100) cc_final: 0.7817 (m100) REVERT: D 414 PHE cc_start: 0.9133 (m-10) cc_final: 0.8910 (m-10) REVERT: D 420 HIS cc_start: 0.9358 (t-90) cc_final: 0.9026 (t-90) REVERT: E 255 MET cc_start: 0.9337 (mtm) cc_final: 0.9076 (mtp) REVERT: E 368 LEU cc_start: 0.9464 (tp) cc_final: 0.9258 (tp) REVERT: E 369 MET cc_start: 0.9016 (mmp) cc_final: 0.8598 (mmm) REVERT: E 387 MET cc_start: 0.9613 (mmm) cc_final: 0.9351 (mmp) REVERT: E 724 MET cc_start: 0.9652 (tmm) cc_final: 0.9420 (tmm) REVERT: E 740 LEU cc_start: 0.9598 (tt) cc_final: 0.9120 (mp) REVERT: E 755 MET cc_start: 0.9231 (mtm) cc_final: 0.8997 (ptp) REVERT: F 288 GLN cc_start: 0.9497 (tp40) cc_final: 0.9208 (tm-30) REVERT: F 420 HIS cc_start: 0.9328 (t-90) cc_final: 0.9000 (t-90) outliers start: 3 outliers final: 0 residues processed: 208 average time/residue: 0.1448 time to fit residues: 47.8661 Evaluate side-chains 145 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [173, 78, 73, 109, 24, 77, 221, 63, 196, 114, 129] chunk 173 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 623 HIS C 623 HIS E 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.026113 restraints weight = 163240.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.027560 restraints weight = 80747.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.028485 restraints weight = 50800.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.029089 restraints weight = 37142.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.029512 restraints weight = 30171.898| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3129 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= 0.147 Angle : 0.949 30.251 29950 Z= 0.388 Chirality : 0.045 0.326 3462 Planarity : 0.003 0.055 3435 Dihedral : 13.158 170.385 3633 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: 1.12 (0.18), residues: 2379 helix: 2.01 (0.16), residues: 942 sheet: 0.10 (0.26), residues: 402 loop : -0.12 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 320 TYR 0.019 0.002 TYR C 622 PHE 0.013 0.001 PHE F 263 TRP 0.009 0.001 TRP E 512 HIS 0.008 0.001 HIS E 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (21826) covalent geometry : angle 0.94713 / 0.39 (29932) hydrogen bonds : bond 0.03893 / 2.64 ( 979) hydrogen bonds : angle 4.52947 / 3.21 ( 2747) metal coordination : bond 0.00750 / 0.47 ( 12) metal coordination : angle 2.85159 / 2.10 ( 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 189 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.568 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: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9340 (mtm) cc_final: 0.9072 (mtp) REVERT: A 368 LEU cc_start: 0.9545 (tp) cc_final: 0.9300 (tp) REVERT: A 369 MET cc_start: 0.8964 (mmp) cc_final: 0.8517 (mmm) REVERT: A 385 MET cc_start: 0.9391 (mtp) cc_final: 0.9062 (mmm) REVERT: A 387 MET cc_start: 0.9398 (mmp) cc_final: 0.8681 (mmt) REVERT: A 680 CYS cc_start: 0.9342 (m) cc_final: 0.8979 (p) REVERT: A 724 MET cc_start: 0.9749 (tmm) cc_final: 0.9470 (tmm) REVERT: A 741 LEU cc_start: 0.9496 (tp) cc_final: 0.9035 (pp) REVERT: A 755 MET cc_start: 0.9332 (mtm) cc_final: 0.9077 (mtp) REVERT: B 288 GLN cc_start: 0.9247 (tp40) cc_final: 0.8945 (mp10) REVERT: B 420 HIS cc_start: 0.9339 (t-90) cc_final: 0.9003 (t-90) REVERT: C 346 LEU cc_start: 0.9459 (tp) cc_final: 0.9169 (tp) REVERT: C 385 MET cc_start: 0.9297 (mmp) cc_final: 0.8966 (mmm) REVERT: C 724 MET cc_start: 0.9660 (tmm) cc_final: 0.9412 (tmm) REVERT: D 337 ASP cc_start: 0.9173 (p0) cc_final: 0.8590 (t70) REVERT: D 360 TRP cc_start: 0.8428 (m100) cc_final: 0.7852 (m100) REVERT: D 420 HIS cc_start: 0.9354 (t-90) cc_final: 0.8975 (t-90) REVERT: E 255 MET cc_start: 0.9378 (mtm) cc_final: 0.9083 (mtp) REVERT: E 346 LEU cc_start: 0.9388 (tp) cc_final: 0.9139 (tp) REVERT: E 369 MET cc_start: 0.9126 (mmp) cc_final: 0.8861 (mmm) REVERT: E 385 MET cc_start: 0.9254 (mmp) cc_final: 0.8866 (mmm) REVERT: E 724 MET cc_start: 0.9670 (tmm) cc_final: 0.9430 (tmm) REVERT: E 740 LEU cc_start: 0.9551 (tt) cc_final: 0.9149 (mp) REVERT: E 755 MET cc_start: 0.9302 (mtm) cc_final: 0.9023 (ptp) REVERT: F 420 HIS cc_start: 0.9310 (t-90) cc_final: 0.8970 (t-90) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1505 time to fit residues: 44.6334 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 : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [11, 94, 19, 3, 202, 177, 178, 56, 160, 206, 43] chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 19 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 160 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN A 623 HIS C 298 ASN C 306 GLN C 623 HIS ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 GLN E 517 GLN F 321 ASN F 423 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.026572 restraints weight = 159175.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.027987 restraints weight = 78581.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.028955 restraints weight = 49449.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.029579 restraints weight = 35829.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.030018 restraints weight = 28918.322| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21838 Z= 0.121 Angle : 0.926 29.768 29950 Z= 0.375 Chirality : 0.045 0.330 3462 Planarity : 0.003 0.059 3435 Dihedral : 12.895 169.849 3633 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.74 % 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: 1.28 (0.18), residues: 2379 helix: 2.14 (0.17), residues: 945 sheet: -0.01 (0.26), residues: 432 loop : 0.08 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 291 TYR 0.019 0.001 TYR F 400 PHE 0.014 0.001 PHE F 263 TRP 0.014 0.001 TRP D 292 HIS 0.005 0.001 HIS E 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (21826) covalent geometry : angle 0.92407 / 0.37 (29932) hydrogen bonds : bond 0.03607 / 2.45 ( 979) hydrogen bonds : angle 4.38679 / 3.10 ( 2747) metal coordination : bond 0.00527 / 0.33 ( 12) metal coordination : angle 2.52386 / 1.84 ( 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 199 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 0.833 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: 0.9355 (mtm) cc_final: 0.9072 (mtp) REVERT: A 368 LEU cc_start: 0.9559 (tp) cc_final: 0.9320 (tp) REVERT: A 369 MET cc_start: 0.9080 (mmp) cc_final: 0.8613 (mmm) REVERT: A 385 MET cc_start: 0.9384 (mtp) cc_final: 0.9069 (mmm) REVERT: A 387 MET cc_start: 0.9364 (mmp) cc_final: 0.8652 (mmt) REVERT: A 680 CYS cc_start: 0.9330 (m) cc_final: 0.9012 (p) REVERT: A 724 MET cc_start: 0.9756 (tmm) cc_final: 0.9487 (tmm) REVERT: A 741 LEU cc_start: 0.9485 (tp) cc_final: 0.8947 (pp) REVERT: A 755 MET cc_start: 0.9328 (mtm) cc_final: 0.9061 (mtp) REVERT: B 288 GLN cc_start: 0.9223 (tp40) cc_final: 0.8918 (tp40) REVERT: B 420 HIS cc_start: 0.9294 (t-90) cc_final: 0.8944 (t-90) REVERT: C 346 LEU cc_start: 0.9495 (tp) cc_final: 0.9221 (tp) REVERT: C 385 MET cc_start: 0.9293 (mmp) cc_final: 0.8974 (mmm) REVERT: C 724 MET cc_start: 0.9662 (tmm) cc_final: 0.9432 (tmm) REVERT: D 263 PHE cc_start: 0.8428 (m-80) cc_final: 0.8150 (m-80) REVERT: D 360 TRP cc_start: 0.8358 (m100) cc_final: 0.7896 (m100) REVERT: D 420 HIS cc_start: 0.9297 (t-90) cc_final: 0.8906 (t-90) REVERT: D 427 ILE cc_start: 0.8383 (pt) cc_final: 0.7724 (pt) REVERT: E 255 MET cc_start: 0.9384 (mtm) cc_final: 0.9070 (mtp) REVERT: E 346 LEU cc_start: 0.9378 (tp) cc_final: 0.9128 (tp) REVERT: E 369 MET cc_start: 0.9108 (mmp) cc_final: 0.8792 (mmm) REVERT: E 385 MET cc_start: 0.9253 (mmp) cc_final: 0.8871 (mmm) REVERT: E 724 MET cc_start: 0.9653 (tmm) cc_final: 0.9412 (tmm) REVERT: E 740 LEU cc_start: 0.9491 (tt) cc_final: 0.9134 (mp) REVERT: E 755 MET cc_start: 0.9302 (mtm) cc_final: 0.9021 (ptp) REVERT: F 420 HIS cc_start: 0.9323 (t-90) cc_final: 0.8991 (t-90) REVERT: F 426 ILE cc_start: 0.9435 (mp) cc_final: 0.9196 (mp) outliers start: 3 outliers final: 0 residues processed: 199 average time/residue: 0.1441 time to fit residues: 44.9947 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 : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [166, 4, 50, 124, 98, 115, 44, 209, 215, 177, 245] chunk 166 optimal weight: 0.8980 chunk 4 optimal weight: 0.0570 chunk 50 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 209 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 623 HIS E 404 GLN E 517 GLN F 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.039941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.026762 restraints weight = 158907.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.028227 restraints weight = 79143.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.029191 restraints weight = 49804.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.029811 restraints weight = 36345.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.030210 restraints weight = 29239.619| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21838 Z= 0.114 Angle : 0.922 29.884 29950 Z= 0.372 Chirality : 0.045 0.327 3462 Planarity : 0.003 0.061 3435 Dihedral : 12.769 170.173 3633 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.05 % Allowed : 1.64 % Favored : 98.31 % 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: 1.36 (0.18), residues: 2379 helix: 2.22 (0.17), residues: 939 sheet: 0.01 (0.26), residues: 432 loop : 0.14 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 296 TYR 0.014 0.001 TYR A 756 PHE 0.017 0.001 PHE F 389 TRP 0.012 0.001 TRP D 292 HIS 0.004 0.001 HIS E 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (21826) covalent geometry : angle 0.92078 / 0.37 (29932) hydrogen bonds : bond 0.03488 / 2.39 ( 979) hydrogen bonds : angle 4.29588 / 3.04 ( 2747) metal coordination : bond 0.00466 / 0.29 ( 12) metal coordination : angle 2.19582 / 1.60 ( 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 189 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.835 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: symmetry clash REVERT: A 255 MET cc_start: 0.9409 (mtm) cc_final: 0.9110 (mtp) REVERT: A 368 LEU cc_start: 0.9565 (tp) cc_final: 0.9332 (tp) REVERT: A 369 MET cc_start: 0.9098 (mmp) cc_final: 0.8669 (mmm) REVERT: A 385 MET cc_start: 0.9386 (mtp) cc_final: 0.9070 (mmm) REVERT: A 387 MET cc_start: 0.9338 (mmp) cc_final: 0.8622 (mmt) REVERT: A 680 CYS cc_start: 0.9334 (m) cc_final: 0.8979 (p) REVERT: A 724 MET cc_start: 0.9759 (tmm) cc_final: 0.9481 (tmm) REVERT: A 741 LEU cc_start: 0.9503 (tp) cc_final: 0.8810 (pp) REVERT: A 755 MET cc_start: 0.9346 (mtm) cc_final: 0.9095 (mtp) REVERT: B 288 GLN cc_start: 0.9229 (tp40) cc_final: 0.8960 (tp40) REVERT: B 420 HIS cc_start: 0.9341 (t-90) cc_final: 0.9009 (t-90) REVERT: B 427 ILE cc_start: 0.8526 (pt) cc_final: 0.7887 (pt) REVERT: C 346 LEU cc_start: 0.9498 (tp) cc_final: 0.9233 (tp) REVERT: C 385 MET cc_start: 0.9280 (mmp) cc_final: 0.8952 (mmm) REVERT: C 724 MET cc_start: 0.9655 (tmm) cc_final: 0.9328 (tmm) REVERT: C 741 LEU cc_start: 0.9328 (tp) cc_final: 0.8800 (pp) REVERT: C 755 MET cc_start: 0.9069 (ptp) cc_final: 0.8601 (ptp) REVERT: D 263 PHE cc_start: 0.8448 (m-80) cc_final: 0.8127 (m-80) REVERT: D 360 TRP cc_start: 0.8355 (m100) cc_final: 0.7885 (m100) REVERT: D 386 LYS cc_start: 0.8509 (pttm) cc_final: 0.8166 (mmmt) REVERT: D 420 HIS cc_start: 0.9285 (t-90) cc_final: 0.8903 (t-90) REVERT: D 427 ILE cc_start: 0.8453 (pt) cc_final: 0.7951 (pt) REVERT: E 255 MET cc_start: 0.9404 (mtm) cc_final: 0.9090 (mtp) REVERT: E 346 LEU cc_start: 0.9393 (tp) cc_final: 0.9158 (tp) REVERT: E 369 MET cc_start: 0.9128 (mmp) cc_final: 0.8761 (mmm) REVERT: E 385 MET cc_start: 0.9256 (mmp) cc_final: 0.8863 (mmm) REVERT: E 387 MET cc_start: 0.9609 (mmm) cc_final: 0.9188 (mmm) REVERT: E 724 MET cc_start: 0.9625 (tmm) cc_final: 0.9404 (tmm) REVERT: E 740 LEU cc_start: 0.9435 (tt) cc_final: 0.9131 (mp) REVERT: E 755 MET cc_start: 0.9323 (mtm) cc_final: 0.9024 (ptp) REVERT: F 420 HIS cc_start: 0.9351 (t-90) cc_final: 0.9030 (t-90) REVERT: F 427 ILE cc_start: 0.8917 (pt) cc_final: 0.8479 (pt) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1445 time to fit residues: 43.5501 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 : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [25, 170, 249, 192, 57, 247, 142, 169, 26, 27, 245] chunk 25 optimal weight: 0.4980 chunk 170 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 57 optimal weight: 0.2980 chunk 247 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 517 GLN F 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.039578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.026503 restraints weight = 160402.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.027942 restraints weight = 79707.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.028886 restraints weight = 50150.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.029493 restraints weight = 36600.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.029907 restraints weight = 29647.112| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21838 Z= 0.132 Angle : 0.927 30.253 29950 Z= 0.375 Chirality : 0.044 0.320 3462 Planarity : 0.003 0.061 3435 Dihedral : 12.795 171.790 3633 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: 1.37 (0.18), residues: 2379 helix: 2.22 (0.17), residues: 939 sheet: 0.06 (0.27), residues: 387 loop : 0.11 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 296 TYR 0.014 0.001 TYR A 756 PHE 0.018 0.001 PHE E 776 TRP 0.011 0.001 TRP D 257 HIS 0.005 0.001 HIS E 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (21826) covalent geometry : angle 0.92514 / 0.38 (29932) hydrogen bonds : bond 0.03541 / 2.43 ( 979) hydrogen bonds : angle 4.29080 / 3.04 ( 2747) metal coordination : bond 0.00652 / 0.40 ( 12) metal coordination : angle 2.41956 / 1.73 ( 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 188 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.718 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: 0.9418 (mtm) cc_final: 0.9106 (mtp) REVERT: A 368 LEU cc_start: 0.9568 (tp) cc_final: 0.9341 (tp) REVERT: A 369 MET cc_start: 0.9110 (mmp) cc_final: 0.8627 (mmm) REVERT: A 385 MET cc_start: 0.9389 (mtp) cc_final: 0.9081 (mmm) REVERT: A 387 MET cc_start: 0.9347 (mmp) cc_final: 0.8643 (mmt) REVERT: A 680 CYS cc_start: 0.9352 (m) cc_final: 0.8976 (p) REVERT: A 724 MET cc_start: 0.9766 (tmm) cc_final: 0.9481 (tmm) REVERT: A 741 LEU cc_start: 0.9395 (tp) cc_final: 0.8712 (pp) REVERT: A 755 MET cc_start: 0.9388 (mtm) cc_final: 0.9090 (mtp) REVERT: B 288 GLN cc_start: 0.9233 (tp40) cc_final: 0.8964 (tp40) REVERT: B 420 HIS cc_start: 0.9301 (t-90) cc_final: 0.8985 (t-90) REVERT: B 427 ILE cc_start: 0.8616 (pt) cc_final: 0.7987 (pt) REVERT: C 255 MET cc_start: 0.9406 (mtm) cc_final: 0.9204 (mtp) REVERT: C 346 LEU cc_start: 0.9484 (tp) cc_final: 0.9229 (tp) REVERT: C 385 MET cc_start: 0.9284 (mmp) cc_final: 0.8960 (mmm) REVERT: C 724 MET cc_start: 0.9647 (tmm) cc_final: 0.9295 (tmm) REVERT: C 741 LEU cc_start: 0.9233 (tp) cc_final: 0.8659 (pp) REVERT: D 263 PHE cc_start: 0.8431 (m-80) cc_final: 0.8098 (m-80) REVERT: D 288 GLN cc_start: 0.9423 (tp40) cc_final: 0.9222 (tp40) REVERT: D 360 TRP cc_start: 0.8349 (m100) cc_final: 0.7919 (m100) REVERT: D 386 LYS cc_start: 0.8546 (pttm) cc_final: 0.8203 (mmmt) REVERT: D 420 HIS cc_start: 0.9185 (t-90) cc_final: 0.8789 (t-90) REVERT: D 427 ILE cc_start: 0.8495 (pt) cc_final: 0.7885 (pt) REVERT: E 255 MET cc_start: 0.9423 (mtm) cc_final: 0.9097 (mtp) REVERT: E 346 LEU cc_start: 0.9405 (tp) cc_final: 0.9197 (tp) REVERT: E 369 MET cc_start: 0.9189 (mmp) cc_final: 0.8814 (mmm) REVERT: E 385 MET cc_start: 0.9254 (mmp) cc_final: 0.8883 (mmm) REVERT: E 520 CYS cc_start: 0.9469 (m) cc_final: 0.9257 (m) REVERT: E 724 MET cc_start: 0.9646 (tmm) cc_final: 0.9404 (tmm) REVERT: E 740 LEU cc_start: 0.9433 (tt) cc_final: 0.9164 (mp) REVERT: E 755 MET cc_start: 0.9356 (mtm) cc_final: 0.9053 (ptp) REVERT: F 420 HIS cc_start: 0.9364 (t-90) cc_final: 0.9078 (t70) REVERT: F 427 ILE cc_start: 0.8983 (pt) cc_final: 0.8478 (pt) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1370 time to fit residues: 41.1649 Evaluate side-chains 139 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [20, 59, 239, 28, 93, 71, 95, 69, 186, 201, 40] chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 0.0040 chunk 71 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 40 optimal weight: 0.0470 overall best weight: 0.6092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 GLN E 517 GLN F 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.027404 restraints weight = 156331.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.028914 restraints weight = 77240.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.029902 restraints weight = 48139.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.030545 restraints weight = 34896.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.030968 restraints weight = 28028.704| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21838 Z= 0.102 Angle : 0.914 29.797 29950 Z= 0.369 Chirality : 0.045 0.332 3462 Planarity : 0.003 0.063 3435 Dihedral : 12.468 170.064 3633 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 1.49 (0.18), residues: 2379 helix: 2.31 (0.17), residues: 933 sheet: 0.04 (0.25), residues: 444 loop : 0.27 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 296 TYR 0.013 0.001 TYR A 756 PHE 0.014 0.001 PHE F 389 TRP 0.032 0.001 TRP F 360 HIS 0.003 0.000 HIS E 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (21826) covalent geometry : angle 0.91319 / 0.37 (29932) hydrogen bonds : bond 0.03323 / 2.27 ( 979) hydrogen bonds : angle 4.20790 / 2.99 ( 2747) metal coordination : bond 0.00240 / 0.15 ( 12) metal coordination : angle 2.12163 / 1.48 ( 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 196 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.856 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: A 255 MET cc_start: 0.9426 (mtm) cc_final: 0.9111 (mtp) REVERT: A 368 LEU cc_start: 0.9558 (tp) cc_final: 0.9254 (tp) REVERT: A 369 MET cc_start: 0.9097 (mmp) cc_final: 0.8518 (mmm) REVERT: A 385 MET cc_start: 0.9369 (mtp) cc_final: 0.9058 (mmm) REVERT: A 387 MET cc_start: 0.9265 (mmp) cc_final: 0.8554 (mmt) REVERT: A 521 MET cc_start: 0.9424 (mtm) cc_final: 0.9160 (mpp) REVERT: A 680 CYS cc_start: 0.9269 (m) cc_final: 0.8977 (p) REVERT: A 724 MET cc_start: 0.9742 (tmm) cc_final: 0.9462 (tmm) REVERT: A 755 MET cc_start: 0.9345 (mtm) cc_final: 0.9075 (mtp) REVERT: B 288 GLN cc_start: 0.9230 (tp40) cc_final: 0.8965 (tp40) REVERT: B 420 HIS cc_start: 0.9289 (t-90) cc_final: 0.8985 (t-90) REVERT: B 427 ILE cc_start: 0.8662 (pt) cc_final: 0.8049 (pt) REVERT: C 255 MET cc_start: 0.9378 (mtm) cc_final: 0.9168 (mtp) REVERT: C 346 LEU cc_start: 0.9495 (tp) cc_final: 0.9260 (tp) REVERT: C 385 MET cc_start: 0.9238 (mmp) cc_final: 0.8915 (mmm) REVERT: C 724 MET cc_start: 0.9623 (tmm) cc_final: 0.9264 (tmm) REVERT: C 741 LEU cc_start: 0.9208 (tp) cc_final: 0.8500 (pp) REVERT: D 263 PHE cc_start: 0.8476 (m-80) cc_final: 0.8098 (m-80) REVERT: D 360 TRP cc_start: 0.8418 (m100) cc_final: 0.8027 (m100) REVERT: D 386 LYS cc_start: 0.8544 (pttm) cc_final: 0.8226 (tptp) REVERT: D 420 HIS cc_start: 0.9248 (t-90) cc_final: 0.8906 (t-90) REVERT: D 426 ILE cc_start: 0.9426 (mp) cc_final: 0.9151 (mp) REVERT: E 255 MET cc_start: 0.9412 (mtm) cc_final: 0.9073 (mtp) REVERT: E 346 LEU cc_start: 0.9406 (tp) cc_final: 0.9199 (tp) REVERT: E 368 LEU cc_start: 0.9568 (tp) cc_final: 0.9353 (tp) REVERT: E 369 MET cc_start: 0.9180 (mmp) cc_final: 0.8765 (mmm) REVERT: E 385 MET cc_start: 0.9219 (mmp) cc_final: 0.8841 (mmm) REVERT: E 520 CYS cc_start: 0.9403 (m) cc_final: 0.9196 (m) REVERT: E 724 MET cc_start: 0.9617 (tmm) cc_final: 0.9377 (tmm) REVERT: E 755 MET cc_start: 0.9339 (mtm) cc_final: 0.9093 (ptp) REVERT: F 420 HIS cc_start: 0.9364 (t-90) cc_final: 0.9080 (t70) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1308 time to fit residues: 41.8626 Evaluate side-chains 147 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [187, 43, 89, 159, 144, 78, 108, 246, 69, 129, 83] chunk 187 optimal weight: 0.0980 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 HIS D 423 ASN E 517 GLN F 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.025073 restraints weight = 165301.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.026400 restraints weight = 82584.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.027314 restraints weight = 52537.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.027896 restraints weight = 38182.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.028304 restraints weight = 30888.860| |-----------------------------------------------------------------------------| r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21838 Z= 0.279 Angle : 1.047 32.361 29950 Z= 0.444 Chirality : 0.048 0.301 3462 Planarity : 0.004 0.057 3435 Dihedral : 13.153 175.569 3633 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 0.97 (0.17), residues: 2379 helix: 1.76 (0.16), residues: 933 sheet: -0.12 (0.26), residues: 399 loop : 0.03 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 291 TYR 0.034 0.002 TYR E 622 PHE 0.019 0.002 PHE A 314 TRP 0.013 0.002 TRP B 360 HIS 0.010 0.002 HIS E 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.28 (21826) covalent geometry : angle 1.04304 / 0.44 (29932) hydrogen bonds : bond 0.04470 / 3.05 ( 979) hydrogen bonds : angle 4.66141 / 3.32 ( 2747) metal coordination : bond 0.01743 / 1.11 ( 12) metal coordination : angle 3.71790 / 2.65 ( 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 162 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.766 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: 0.9457 (mtm) cc_final: 0.9140 (mtp) REVERT: A 368 LEU cc_start: 0.9494 (tp) cc_final: 0.9245 (tp) REVERT: A 369 MET cc_start: 0.9197 (mmp) cc_final: 0.8736 (mmm) REVERT: A 385 MET cc_start: 0.9437 (mtp) cc_final: 0.9065 (mmm) REVERT: A 387 MET cc_start: 0.9393 (mmp) cc_final: 0.8688 (mmt) REVERT: A 724 MET cc_start: 0.9783 (tmm) cc_final: 0.9408 (tmm) REVERT: A 741 LEU cc_start: 0.9358 (tp) cc_final: 0.8605 (pp) REVERT: A 755 MET cc_start: 0.9474 (mtm) cc_final: 0.9118 (mtp) REVERT: B 288 GLN cc_start: 0.9115 (tp40) cc_final: 0.8840 (tp40) REVERT: B 337 ASP cc_start: 0.9226 (p0) cc_final: 0.8675 (t70) REVERT: B 386 LYS cc_start: 0.8595 (pttm) cc_final: 0.8279 (tptt) REVERT: B 401 GLU cc_start: 0.8796 (pm20) cc_final: 0.8535 (mp0) REVERT: B 420 HIS cc_start: 0.9229 (t-90) cc_final: 0.8891 (t-90) REVERT: B 427 ILE cc_start: 0.8703 (pt) cc_final: 0.8080 (pt) REVERT: C 255 MET cc_start: 0.9468 (mtm) cc_final: 0.9236 (mtp) REVERT: C 385 MET cc_start: 0.9275 (mmp) cc_final: 0.8927 (mmm) REVERT: C 724 MET cc_start: 0.9665 (tmm) cc_final: 0.9384 (tmm) REVERT: C 741 LEU cc_start: 0.9241 (tp) cc_final: 0.8579 (pp) REVERT: D 263 PHE cc_start: 0.8393 (m-80) cc_final: 0.8001 (m-80) REVERT: D 337 ASP cc_start: 0.9275 (p0) cc_final: 0.8782 (t70) REVERT: D 360 TRP cc_start: 0.8391 (m100) cc_final: 0.7904 (m100) REVERT: D 386 LYS cc_start: 0.8503 (pttm) cc_final: 0.8166 (tptp) REVERT: D 420 HIS cc_start: 0.9157 (t-90) cc_final: 0.8732 (t-90) REVERT: D 426 ILE cc_start: 0.9347 (mp) cc_final: 0.9101 (mp) REVERT: D 427 ILE cc_start: 0.8617 (pt) cc_final: 0.8029 (pt) REVERT: E 255 MET cc_start: 0.9462 (mtm) cc_final: 0.9092 (mtp) REVERT: E 369 MET cc_start: 0.9198 (mmp) cc_final: 0.8790 (mmm) REVERT: E 385 MET cc_start: 0.9267 (mmp) cc_final: 0.8866 (mmm) REVERT: E 724 MET cc_start: 0.9689 (tmm) cc_final: 0.9453 (tmm) REVERT: E 755 MET cc_start: 0.9490 (mtm) cc_final: 0.9146 (mtp) REVERT: F 420 HIS cc_start: 0.9287 (t-90) cc_final: 0.8973 (t-90) REVERT: F 427 ILE cc_start: 0.9021 (pt) cc_final: 0.8565 (pt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1382 time to fit residues: 36.6050 Evaluate side-chains 124 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [8, 119, 57, 235, 166, 145, 147, 217, 15, 0, 73] chunk 8 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 HIS E 517 GLN F 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.038856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.025817 restraints weight = 162944.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.027250 restraints weight = 81907.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.028194 restraints weight = 51637.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.028790 restraints weight = 37724.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.029190 restraints weight = 30568.917| |-----------------------------------------------------------------------------| r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21838 Z= 0.147 Angle : 0.949 30.269 29950 Z= 0.389 Chirality : 0.046 0.317 3462 Planarity : 0.003 0.059 3435 Dihedral : 12.958 172.785 3633 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: 1.23 (0.18), residues: 2379 helix: 2.13 (0.17), residues: 930 sheet: -0.11 (0.26), residues: 411 loop : 0.08 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 791 TYR 0.031 0.002 TYR E 622 PHE 0.016 0.001 PHE E 776 TRP 0.015 0.001 TRP B 360 HIS 0.004 0.001 HIS E 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (21826) covalent geometry : angle 0.94613 / 0.39 (29932) hydrogen bonds : bond 0.03581 / 2.46 ( 979) hydrogen bonds : angle 4.38743 / 3.12 ( 2747) metal coordination : bond 0.00887 / 0.56 ( 12) metal coordination : angle 2.94891 / 2.13 ( 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 : 0.598 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: 0.9453 (mtm) cc_final: 0.9138 (mtp) REVERT: A 368 LEU cc_start: 0.9521 (tp) cc_final: 0.9282 (tp) REVERT: A 369 MET cc_start: 0.9220 (mmp) cc_final: 0.8662 (mmm) REVERT: A 385 MET cc_start: 0.9423 (mtp) cc_final: 0.9052 (mmm) REVERT: A 387 MET cc_start: 0.9355 (mmp) cc_final: 0.8629 (mmt) REVERT: A 680 CYS cc_start: 0.9243 (m) cc_final: 0.8855 (p) REVERT: A 724 MET cc_start: 0.9779 (tmm) cc_final: 0.9445 (tmm) REVERT: A 741 LEU cc_start: 0.9328 (tp) cc_final: 0.8610 (pp) REVERT: A 755 MET cc_start: 0.9467 (mtm) cc_final: 0.9100 (mtp) REVERT: B 288 GLN cc_start: 0.9164 (tp40) cc_final: 0.8890 (tp40) REVERT: B 420 HIS cc_start: 0.9241 (t-90) cc_final: 0.8917 (t-90) REVERT: B 427 ILE cc_start: 0.8616 (pt) cc_final: 0.7960 (pt) REVERT: C 255 MET cc_start: 0.9450 (mtm) cc_final: 0.9209 (mtp) REVERT: C 385 MET cc_start: 0.9274 (mmp) cc_final: 0.8950 (mmm) REVERT: C 724 MET cc_start: 0.9649 (tmm) cc_final: 0.9291 (tmm) REVERT: C 741 LEU cc_start: 0.9212 (tp) cc_final: 0.8504 (pp) REVERT: C 776 PHE cc_start: 0.9195 (t80) cc_final: 0.8991 (t80) REVERT: D 263 PHE cc_start: 0.8416 (m-80) cc_final: 0.7994 (m-80) REVERT: D 297 PHE cc_start: 0.8647 (m-80) cc_final: 0.8356 (m-10) REVERT: D 360 TRP cc_start: 0.8426 (m100) cc_final: 0.7980 (m100) REVERT: D 420 HIS cc_start: 0.9098 (t-90) cc_final: 0.8666 (t-90) REVERT: D 426 ILE cc_start: 0.9355 (mp) cc_final: 0.9098 (mp) REVERT: D 427 ILE cc_start: 0.8712 (pt) cc_final: 0.8183 (pt) REVERT: E 255 MET cc_start: 0.9470 (mtm) cc_final: 0.9107 (mtp) REVERT: E 346 LEU cc_start: 0.9365 (tp) cc_final: 0.9125 (tp) REVERT: E 369 MET cc_start: 0.9287 (mmp) cc_final: 0.8873 (mmm) REVERT: E 385 MET cc_start: 0.9256 (mmp) cc_final: 0.8872 (mmm) REVERT: E 521 MET cc_start: 0.9330 (ptp) cc_final: 0.9120 (pmm) REVERT: E 724 MET cc_start: 0.9648 (tmm) cc_final: 0.9406 (tmm) REVERT: E 755 MET cc_start: 0.9461 (mtm) cc_final: 0.9130 (mtp) REVERT: F 420 HIS cc_start: 0.9275 (t-90) cc_final: 0.8959 (t-90) REVERT: F 427 ILE cc_start: 0.8933 (pt) cc_final: 0.8414 (pt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1317 time to fit residues: 37.3251 Evaluate side-chains 133 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: [177, 147, 87, 194, 213, 126, 145, 148, 232, 127, 167] chunk 177 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 341 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 HIS E 341 ASN E 517 GLN F 321 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.037483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.024781 restraints weight = 169496.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.026135 restraints weight = 85418.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.027018 restraints weight = 54121.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.027582 restraints weight = 39548.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.027947 restraints weight = 32158.574| |-----------------------------------------------------------------------------| r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 21838 Z= 0.281 Angle : 1.051 31.656 29950 Z= 0.448 Chirality : 0.048 0.313 3462 Planarity : 0.004 0.051 3435 Dihedral : 13.284 174.473 3633 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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: 0.72 (0.17), residues: 2379 helix: 1.52 (0.16), residues: 933 sheet: -0.31 (0.26), residues: 402 loop : -0.04 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 732 TYR 0.035 0.002 TYR E 622 PHE 0.019 0.002 PHE E 314 TRP 0.014 0.002 TRP B 360 HIS 0.014 0.002 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.28 (21826) covalent geometry : angle 1.04669 / 0.45 (29932) hydrogen bonds : bond 0.04416 / 3.02 ( 979) hydrogen bonds : angle 4.79291 / 3.41 ( 2747) metal coordination : bond 0.01840 / 1.17 ( 12) metal coordination : angle 4.01930 / 2.90 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3486.56 seconds wall clock time: 61 minutes 11.07 seconds (3671.07 seconds total)