Starting phenix.real_space_refine on Mon Jul 6 23:49:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vc0_31887/07_2026/7vc0_31887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vc0_31887/07_2026/7vc0_31887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vc0_31887/07_2026/7vc0_31887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vc0_31887/07_2026/7vc0_31887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vc0_31887/07_2026/7vc0_31887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vc0_31887/07_2026/7vc0_31887.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vc0_31887/07_2026/7vc0_31887.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vc0_31887/07_2026/7vc0_31887.cif" } resolution = 2.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 293 5.16 5 C 26037 2.51 5 N 6288 2.21 5 O 7396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40048 Number of models: 1 Model: "" Number of chains: 69 Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 7, 'TRANS': 36} Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 949 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "X" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 703 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "m" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1298 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1062 Unusual residues: {'MYR': 1} Classifications: {'peptide': 124, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116, None: 1} Not linked: pdbres="MYR v 1 " pdbres="GLY v 2 " Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'MYR:plan-1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "w" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2590 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "Q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 94 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 184 Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "n" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 278 Unusual residues: {'CDL': 2, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "s" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {' UQ': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "u" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "i" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "j" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "k" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "l" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "m" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "n" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "s" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 8.08, per 1000 atoms: 0.20 Number of scatterers: 40048 At special positions: 0 Unit cell: (186.911, 187.448, 139.109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 293 16.00 P 34 15.00 O 7396 8.00 N 6288 7.00 C 26037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.02 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.04 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.6 seconds 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8956 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 5 sheets defined 71.2% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'Q' and resid 40 through 45 Processing helix chain 'Q' and resid 46 through 48 No H-bonds generated for 'chain 'Q' and resid 46 through 48' Processing helix chain 'Q' and resid 57 through 61 removed outlier: 3.814A pdb=" N HIS Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 1 through 4 Processing helix chain 'S' and resid 5 through 30 removed outlier: 3.616A pdb=" N ILE S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 41 through 56 removed outlier: 4.187A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 removed outlier: 3.687A pdb=" N ILE S 69 " --> pdb=" O LEU S 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 16 Processing helix chain 'U' and resid 16 through 32 Processing helix chain 'U' and resid 33 through 36 Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 78 through 83 removed outlier: 3.520A pdb=" N ASN U 83 " --> pdb=" O GLU U 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 17 through 44 Processing helix chain 'V' and resid 48 through 82 Processing helix chain 'V' and resid 86 through 106 removed outlier: 4.173A pdb=" N TYR V 90 " --> pdb=" O ASP V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 132 Processing helix chain 'W' and resid 33 through 98 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 120 through 125 Processing helix chain 'W' and resid 129 through 143 removed outlier: 6.437A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 89 Processing helix chain 'X' and resid 111 through 127 Processing helix chain 'X' and resid 131 through 136 Processing helix chain 'X' and resid 140 through 152 Processing helix chain 'Y' and resid 51 through 76 removed outlier: 3.680A pdb=" N LEU Y 55 " --> pdb=" O THR Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 82 Processing helix chain 'Y' and resid 88 through 92 Processing helix chain 'Y' and resid 93 through 98 Processing helix chain 'Z' and resid 18 through 22 removed outlier: 3.525A pdb=" N GLN Z 21 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP Z 22 " --> pdb=" O TYR Z 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 18 through 22' Processing helix chain 'Z' and resid 27 through 38 removed outlier: 3.657A pdb=" N THR Z 31 " --> pdb=" O THR Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 50 removed outlier: 3.606A pdb=" N GLU Z 49 " --> pdb=" O TRP Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 55 removed outlier: 4.277A pdb=" N GLY Z 55 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 68 Processing helix chain 'Z' and resid 70 through 89 Processing helix chain 'a' and resid 61 through 93 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 108 through 113 removed outlier: 3.671A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE a 113 " --> pdb=" O TRP a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 115 through 126 Processing helix chain 'a' and resid 128 through 164 removed outlier: 4.126A pdb=" N ASN a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 Processing helix chain 'b' and resid 5 through 25 Processing helix chain 'b' and resid 68 through 74 removed outlier: 3.583A pdb=" N VAL b 72 " --> pdb=" O SER b 68 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR b 73 " --> pdb=" O ILE b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'b' and resid 90 through 93 Processing helix chain 'c' and resid 33 through 37 removed outlier: 3.516A pdb=" N MET c 36 " --> pdb=" O THR c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 82 through 86 Processing helix chain 'c' and resid 108 through 112 Processing helix chain 'c' and resid 128 through 150 Processing helix chain 'd' and resid 28 through 58 removed outlier: 4.829A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 73 through 77 Processing helix chain 'd' and resid 81 through 118 removed outlier: 3.854A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 125 through 144 Processing helix chain 'd' and resid 151 through 175 Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.427A pdb=" N LYS e 69 " --> pdb=" O ASN e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 96 Processing helix chain 'e' and resid 98 through 108 Processing helix chain 'e' and resid 114 through 132 Processing helix chain 'e' and resid 143 through 147 Processing helix chain 'f' and resid 40 through 74 Processing helix chain 'g' and resid 18 through 23 Processing helix chain 'g' and resid 30 through 51 Processing helix chain 'g' and resid 59 through 99 removed outlier: 3.786A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 103 Processing helix chain 'g' and resid 110 through 114 removed outlier: 3.516A pdb=" N ILE g 114 " --> pdb=" O TYR g 111 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.503A pdb=" N ARG h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 15 through 19 Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 45 Processing helix chain 'h' and resid 48 through 56 removed outlier: 3.874A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 56 through 69 Processing helix chain 'h' and resid 69 through 89 Processing helix chain 'h' and resid 95 through 99 Processing helix chain 'i' and resid 2 through 23 Processing helix chain 'i' and resid 25 through 45 Proline residue: i 42 - end of helix removed outlier: 3.550A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 81 Processing helix chain 'i' and resid 91 through 107 Processing helix chain 'i' and resid 113 through 122 removed outlier: 4.319A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 133 Processing helix chain 'i' and resid 135 through 145 Processing helix chain 'i' and resid 146 through 149 Processing helix chain 'i' and resid 150 through 170 Processing helix chain 'i' and resid 174 through 193 removed outlier: 3.892A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 197 through 222 removed outlier: 3.562A pdb=" N THR i 201 " --> pdb=" O ASN i 197 " (cutoff:3.500A) Processing helix chain 'i' and resid 226 through 231 Processing helix chain 'i' and resid 232 through 236 Processing helix chain 'i' and resid 237 through 252 Processing helix chain 'i' and resid 259 through 272 removed outlier: 4.435A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 4.605A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 3.703A pdb=" N LYS i 314 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 325 through 335 Processing helix chain 'i' and resid 336 through 347 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 30 through 35 Processing helix chain 'j' and resid 55 through 73 removed outlier: 3.553A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 79 Processing helix chain 'j' and resid 83 through 108 removed outlier: 3.513A pdb=" N MET j 87 " --> pdb=" O ASN j 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 21 Processing helix chain 'k' and resid 25 through 52 removed outlier: 3.904A pdb=" N SER k 29 " --> pdb=" O HIS k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 57 Processing helix chain 'k' and resid 58 through 86 Processing helix chain 'k' and resid 89 through 93 Processing helix chain 'l' and resid 2 through 14 removed outlier: 4.259A pdb=" N SER l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 21 Processing helix chain 'l' and resid 22 through 29 removed outlier: 6.551A pdb=" N ASN l 25 " --> pdb=" O SER l 22 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE l 26 " --> pdb=" O ASN l 23 " (cutoff:3.500A) Processing helix chain 'l' and resid 31 through 58 removed outlier: 4.241A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 83 through 108 Proline residue: l 91 - end of helix removed outlier: 3.829A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 134 Processing helix chain 'l' and resid 136 through 156 Processing helix chain 'l' and resid 161 through 194 removed outlier: 3.995A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 197 through 205 Processing helix chain 'l' and resid 209 through 224 removed outlier: 4.175A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.745A pdb=" N HIS l 230 " --> pdb=" O PHE l 227 " (cutoff:3.500A) Processing helix chain 'l' and resid 231 through 236 removed outlier: 3.505A pdb=" N SER l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) Processing helix chain 'l' and resid 237 through 239 No H-bonds generated for 'chain 'l' and resid 237 through 239' Processing helix chain 'l' and resid 240 through 247 Processing helix chain 'l' and resid 254 through 263 Processing helix chain 'l' and resid 263 through 268 Processing helix chain 'l' and resid 270 through 293 removed outlier: 3.540A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 4.062A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 355 through 359 Processing helix chain 'l' and resid 366 through 381 Processing helix chain 'l' and resid 386 through 401 removed outlier: 3.700A pdb=" N TYR l 390 " --> pdb=" O LEU l 386 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 405 through 432 removed outlier: 3.705A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 471 removed outlier: 5.878A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 483 through 488 Processing helix chain 'l' and resid 488 through 507 Processing helix chain 'l' and resid 508 through 510 No H-bonds generated for 'chain 'l' and resid 508 through 510' Processing helix chain 'l' and resid 517 through 525 Processing helix chain 'l' and resid 528 through 534 Processing helix chain 'l' and resid 535 through 548 Processing helix chain 'l' and resid 556 through 562 removed outlier: 3.738A pdb=" N LEU l 562 " --> pdb=" O LEU l 558 " (cutoff:3.500A) Processing helix chain 'l' and resid 562 through 579 Processing helix chain 'l' and resid 583 through 602 removed outlier: 3.541A pdb=" N TYR l 587 " --> pdb=" O LEU l 583 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 22 Processing helix chain 'm' and resid 25 through 46 Processing helix chain 'm' and resid 49 through 75 Processing helix chain 'm' and resid 86 through 109 Processing helix chain 'm' and resid 123 through 128 removed outlier: 3.876A pdb=" N VAL m 126 " --> pdb=" O GLY m 123 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR m 128 " --> pdb=" O TRP m 125 " (cutoff:3.500A) Processing helix chain 'm' and resid 137 through 145 Processing helix chain 'm' and resid 150 through 172 Processing helix chain 'n' and resid 4 through 12 Processing helix chain 'n' and resid 15 through 34 removed outlier: 3.628A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 15 through 23 Proline residue: o 20 - end of helix Processing helix chain 'o' and resid 26 through 52 removed outlier: 3.782A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 62 through 74 Processing helix chain 'o' and resid 76 through 80 Processing helix chain 'o' and resid 83 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 11 through 31 Processing helix chain 'p' and resid 33 through 50 Processing helix chain 'p' and resid 56 through 75 Processing helix chain 'p' and resid 94 through 98 Processing helix chain 'p' and resid 100 through 107 Processing helix chain 'p' and resid 108 through 114 removed outlier: 3.715A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 144 removed outlier: 4.915A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'r' and resid 2 through 17 Proline residue: r 7 - end of helix removed outlier: 4.116A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 22 through 39 Processing helix chain 'r' and resid 40 through 43 removed outlier: 3.645A pdb=" N ASN r 43 " --> pdb=" O SER r 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 40 through 43' Processing helix chain 'r' and resid 61 through 81 removed outlier: 4.115A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 88 through 112 removed outlier: 3.620A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 125 through 137 removed outlier: 3.789A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 172 removed outlier: 3.808A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 175 through 182 Processing helix chain 'r' and resid 189 through 207 removed outlier: 4.753A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 4.015A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 224 through 234 Processing helix chain 'r' and resid 234 through 247 removed outlier: 4.084A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) Processing helix chain 'r' and resid 248 through 250 No H-bonds generated for 'chain 'r' and resid 248 through 250' Processing helix chain 'r' and resid 253 through 258 Processing helix chain 'r' and resid 258 through 278 removed outlier: 3.645A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 281 through 304 removed outlier: 3.656A pdb=" N GLN r 304 " --> pdb=" O ALA r 300 " (cutoff:3.500A) Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.635A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 347 through 352 removed outlier: 4.055A pdb=" N LEU r 351 " --> pdb=" O GLY r 347 " (cutoff:3.500A) Processing helix chain 'r' and resid 352 through 367 Processing helix chain 'r' and resid 372 through 389 Processing helix chain 'r' and resid 391 through 416 removed outlier: 4.042A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) Processing helix chain 'r' and resid 430 through 447 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 448 through 449 No H-bonds generated for 'chain 'r' and resid 448 through 449' Processing helix chain 'r' and resid 450 through 455 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.716A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 Processing helix chain 's' and resid 46 through 57 Processing helix chain 's' and resid 67 through 85 Proline residue: s 75 - end of helix Processing helix chain 's' and resid 100 through 124 removed outlier: 3.820A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN s 124 " --> pdb=" O GLY s 120 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 5.194A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 3.797A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 177 Processing helix chain 's' and resid 178 through 193 Processing helix chain 's' and resid 203 through 208 Processing helix chain 's' and resid 209 through 213 removed outlier: 3.758A pdb=" N ASN s 212 " --> pdb=" O SER s 209 " (cutoff:3.500A) Processing helix chain 's' and resid 216 through 243 removed outlier: 3.820A pdb=" N PHE s 220 " --> pdb=" O ALA s 216 " (cutoff:3.500A) Processing helix chain 's' and resid 251 through 277 removed outlier: 4.267A pdb=" N TYR s 255 " --> pdb=" O THR s 251 " (cutoff:3.500A) Processing helix chain 's' and resid 281 through 292 removed outlier: 3.561A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 292 through 311 removed outlier: 3.608A pdb=" N LEU s 296 " --> pdb=" O SER s 292 " (cutoff:3.500A) Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 21 through 36 removed outlier: 4.891A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 51 removed outlier: 3.524A pdb=" N ASN u 40 " --> pdb=" O CYS u 36 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 55 Processing helix chain 'u' and resid 56 through 78 Processing helix chain 'u' and resid 78 through 92 removed outlier: 4.315A pdb=" N PHE u 82 " --> pdb=" O CYS u 78 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 116 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 12 through 16 Processing helix chain 'v' and resid 42 through 50 Processing helix chain 'v' and resid 59 through 73 removed outlier: 3.527A pdb=" N LEU v 63 " --> pdb=" O CYS v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 80 through 124 Processing helix chain 'w' and resid 39 through 45 Processing helix chain 'w' and resid 69 through 82 Processing helix chain 'w' and resid 93 through 98 removed outlier: 3.501A pdb=" N THR w 98 " --> pdb=" O ASP w 95 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 120 Processing helix chain 'w' and resid 126 through 154 Processing helix chain 'w' and resid 166 through 176 removed outlier: 3.812A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 195 Processing helix chain 'w' and resid 196 through 198 No H-bonds generated for 'chain 'w' and resid 196 through 198' Processing helix chain 'w' and resid 210 through 222 removed outlier: 3.689A pdb=" N GLY w 222 " --> pdb=" O ILE w 218 " (cutoff:3.500A) Processing helix chain 'w' and resid 225 through 229 Processing helix chain 'w' and resid 230 through 253 removed outlier: 5.394A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.653A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS w 252 " --> pdb=" O GLU w 248 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 264 removed outlier: 4.061A pdb=" N GLU w 264 " --> pdb=" O ARG w 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 261 through 264' Processing helix chain 'w' and resid 265 through 275 Processing helix chain 'w' and resid 282 through 286 Processing helix chain 'w' and resid 287 through 299 removed outlier: 3.551A pdb=" N GLN w 299 " --> pdb=" O ARG w 295 " (cutoff:3.500A) Processing helix chain 'w' and resid 300 through 306 Processing helix chain 'w' and resid 307 through 310 removed outlier: 3.832A pdb=" N ILE w 310 " --> pdb=" O TYR w 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 307 through 310' Processing helix chain 'w' and resid 320 through 333 Processing helix chain 'w' and resid 340 through 348 removed outlier: 4.112A pdb=" N ASN w 344 " --> pdb=" O PRO w 341 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU w 345 " --> pdb=" O GLY w 342 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP w 346 " --> pdb=" O TYR w 343 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY w 348 " --> pdb=" O GLU w 345 " (cutoff:3.500A) Processing helix chain 'w' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'U' and resid 57 through 58 removed outlier: 6.422A pdb=" N LEU U 57 " --> pdb=" O VAL u 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'a' and resid 97 through 98 removed outlier: 5.924A pdb=" N GLU a 97 " --> pdb=" O TYR d 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'b' and resid 97 through 99 removed outlier: 5.368A pdb=" N SER l 64 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE l 80 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP l 66 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU l 76 " --> pdb=" O TRP l 68 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR l 70 " --> pdb=" O VAL l 74 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL l 74 " --> pdb=" O THR l 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'w' and resid 84 through 85 removed outlier: 6.702A pdb=" N ARG w 84 " --> pdb=" O VAL w 158 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE w 60 " --> pdb=" O LEU w 159 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR w 61 " --> pdb=" O VAL w 205 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL w 207 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP w 63 " --> pdb=" O VAL w 207 " (cutoff:3.500A) 2342 hydrogen bonds defined for protein. 6774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.72 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5996 1.32 - 1.46: 13637 1.46 - 1.60: 20405 1.60 - 1.74: 67 1.74 - 1.88: 530 Bond restraints: 40635 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.295 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C18 UQ s 402 " pdb=" C19 UQ s 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CA7 CDL u 201 " pdb=" OA8 CDL u 201 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.14e+02 bond pdb=" C13 UQ s 402 " pdb=" C14 UQ s 402 " ideal model delta sigma weight residual 1.335 1.548 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CB7 CDL u 201 " pdb=" OB8 CDL u 201 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.10e-02 8.26e+03 1.10e+02 ... (remaining 40630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 54225 3.50 - 7.00: 488 7.00 - 10.49: 95 10.49 - 13.99: 20 13.99 - 17.49: 10 Bond angle restraints: 54838 Sorted by residual: angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.54 -9.21 1.32e+00 5.72e-01 4.86e+01 angle pdb=" C51 CDL s 401 " pdb=" CB5 CDL s 401 " pdb=" OB6 CDL s 401 " ideal model delta sigma weight residual 111.33 120.25 -8.92 1.32e+00 5.72e-01 4.55e+01 angle pdb=" C11 CDL u 201 " pdb=" CA5 CDL u 201 " pdb=" OA6 CDL u 201 " ideal model delta sigma weight residual 111.33 120.17 -8.84 1.32e+00 5.72e-01 4.47e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.15 -8.82 1.32e+00 5.72e-01 4.46e+01 angle pdb=" C51 CDL r 504 " pdb=" CB5 CDL r 504 " pdb=" OB6 CDL r 504 " ideal model delta sigma weight residual 111.33 120.07 -8.74 1.32e+00 5.72e-01 4.37e+01 ... (remaining 54833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 23758 34.99 - 69.98: 726 69.98 - 104.96: 59 104.96 - 139.95: 10 139.95 - 174.94: 14 Dihedral angle restraints: 24567 sinusoidal: 10703 harmonic: 13864 Sorted by residual: dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.48 -168.47 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" CA MET r 207 " pdb=" C MET r 207 " pdb=" N PRO r 208 " pdb=" CA PRO r 208 " ideal model delta harmonic sigma weight residual 0.00 -33.24 33.24 0 5.00e+00 4.00e-02 4.42e+01 dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -142.36 56.36 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 24564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 5379 0.076 - 0.152: 522 0.152 - 0.229: 23 0.229 - 0.305: 3 0.305 - 0.381: 4 Chirality restraints: 5931 Sorted by residual: chirality pdb=" C6 PLX e 201 " pdb=" C7 PLX e 201 " pdb=" O6 PLX e 201 " pdb=" O7 PLX e 201 " both_signs ideal model delta sigma weight residual False 2.01 2.39 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C6 PLX n 101 " pdb=" C7 PLX n 101 " pdb=" O6 PLX n 101 " pdb=" O7 PLX n 101 " both_signs ideal model delta sigma weight residual False 2.01 2.34 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C6 PLX j 202 " pdb=" C7 PLX j 202 " pdb=" O6 PLX j 202 " pdb=" O7 PLX j 202 " both_signs ideal model delta sigma weight residual False 2.01 2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 5928 not shown) Planarity restraints: 6680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.443 2.00e-02 2.50e+03 3.90e-01 1.90e+03 pdb=" C18 UQ s 402 " -0.470 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.407 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.015 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.419 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.074 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C11 UQ s 402 " 0.057 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.291 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.538 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " -0.229 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 402 " -0.132 2.00e-02 2.50e+03 1.86e-01 4.34e+02 pdb=" C13 UQ s 402 " 0.062 2.00e-02 2.50e+03 pdb=" C14 UQ s 402 " 0.329 2.00e-02 2.50e+03 pdb=" C15 UQ s 402 " -0.056 2.00e-02 2.50e+03 pdb=" C16 UQ s 402 " -0.204 2.00e-02 2.50e+03 ... (remaining 6677 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 406 2.60 - 3.17: 33463 3.17 - 3.75: 65879 3.75 - 4.32: 94999 4.32 - 4.90: 150369 Nonbonded interactions: 345116 Sorted by model distance: nonbonded pdb=" OE1 GLN l 580 " pdb=" O HOH l 801 " model vdw 2.024 3.040 nonbonded pdb=" O HOH d 201 " pdb=" O HOH l 844 " model vdw 2.076 3.040 nonbonded pdb=" OE2 GLU h 37 " pdb=" O HOH h 201 " model vdw 2.085 3.040 nonbonded pdb=" O HOH i 448 " pdb=" O HOH i 469 " model vdw 2.089 3.040 nonbonded pdb=" O HOH i 460 " pdb=" O HOH i 470 " model vdw 2.104 3.040 ... (remaining 345111 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.640 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 34.770 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 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 : 0.009 0.899 40646 Z= 0.627 Angle : 0.900 17.488 54854 Z= 0.457 Chirality : 0.046 0.381 5931 Planarity : 0.009 0.390 6680 Dihedral : 16.898 174.939 15587 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.55 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % 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: 1.52 (0.12), residues: 4667 helix: 1.76 (0.09), residues: 2951 sheet: -0.13 (1.12), residues: 25 loop : -0.27 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG s 134 TYR 0.021 0.002 TYR r 406 PHE 0.033 0.002 PHE r 122 TRP 0.019 0.001 TRP u 86 HIS 0.012 0.001 HIS l 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.44 (40635) covalent geometry : angle 0.89958 / 0.46 (54838) SS BOND : bond 0.00494 / 0.29 ( 8) SS BOND : angle 2.27033 / 1.27 ( 16) hydrogen bonds : bond 0.13357 / 9.02 ( 2342) hydrogen bonds : angle 5.55963 / 4.06 ( 6774) Misc. bond : bond 0.51965 / 15.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 819 time to evaluate : 1.631 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: h 80 LYS cc_start: 0.7166 (tttt) cc_final: 0.6573 (pttt) REVERT: r 19 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7761 (mppt) REVERT: s 202 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6695 (tm-30) outliers start: 2 outliers final: 2 residues processed: 821 average time/residue: 0.8628 time to fit residues: 835.1131 Evaluate side-chains 715 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 712 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN U 71 GLN Y 54 GLN d 54 GLN h 70 GLN i 289 ASN l 23 ASN l 534 HIS ** l 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 HIS p 62 GLN r 43 ASN s 287 HIS u 64 ASN u 95 GLN v 43 GLN v 85 HIS w 202 HIS w 219 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.123107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102095 restraints weight = 42718.763| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.06 r_work: 0.2878 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40646 Z= 0.147 Angle : 0.593 10.844 54854 Z= 0.304 Chirality : 0.042 0.196 5931 Planarity : 0.005 0.080 6680 Dihedral : 16.201 167.769 6331 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.81 % Rotamer: Outliers : 1.21 % Allowed : 6.93 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.90 (0.12), residues: 4667 helix: 2.02 (0.09), residues: 3013 sheet: 0.14 (1.10), residues: 25 loop : -0.13 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 158 TYR 0.026 0.001 TYR l 422 PHE 0.030 0.002 PHE r 122 TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS l 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (40635) covalent geometry : angle 0.59196 / 0.30 (54838) SS BOND : bond 0.00439 / 0.27 ( 8) SS BOND : angle 1.67923 / 1.08 ( 16) hydrogen bonds : bond 0.05852 / 3.95 ( 2342) hydrogen bonds : angle 4.42652 / 3.23 ( 6774) Misc. bond : bond 0.00200 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 746 time to evaluate : 1.659 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: W 85 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8683 (tt0) REVERT: X 80 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8693 (ttmt) REVERT: h 80 LYS cc_start: 0.7450 (tttt) cc_final: 0.6661 (pttt) REVERT: j 44 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.6998 (tpp) REVERT: l 544 MET cc_start: 0.9042 (mmp) cc_final: 0.8813 (mmm) REVERT: m 1 MET cc_start: 0.2706 (mtt) cc_final: 0.2314 (mtp) REVERT: m 100 GLU cc_start: 0.8067 (tp30) cc_final: 0.7819 (tp30) REVERT: o 85 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7793 (tptp) REVERT: p 62 GLN cc_start: 0.7947 (tm130) cc_final: 0.6770 (tm-30) REVERT: p 66 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7503 (mp10) REVERT: r 19 LYS cc_start: 0.8492 (mtmm) cc_final: 0.7867 (mppt) REVERT: r 141 GLU cc_start: 0.8902 (mp0) cc_final: 0.8660 (mp0) REVERT: s 202 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: w 295 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8037 (ttt90) REVERT: w 333 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8193 (mt-10) outliers start: 50 outliers final: 13 residues processed: 767 average time/residue: 0.8202 time to fit residues: 745.3220 Evaluate side-chains 722 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 701 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain X residue 80 LYS Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 254 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 295 ARG Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 448 optimal weight: 9.9990 chunk 442 optimal weight: 0.9990 chunk 432 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 449 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 286 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN h 21 GLN l 518 GLN ** l 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 103 GLN s 287 HIS u 95 GLN u 143 HIS v 85 HIS v 110 GLN w 124 ASN w 202 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.119254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.098155 restraints weight = 42412.847| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.03 r_work: 0.2817 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 40646 Z= 0.219 Angle : 0.663 10.546 54854 Z= 0.342 Chirality : 0.047 0.208 5931 Planarity : 0.005 0.074 6680 Dihedral : 15.620 161.639 6326 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.46 % Rotamer: Outliers : 2.04 % Allowed : 8.73 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.73 (0.12), residues: 4667 helix: 1.87 (0.09), residues: 3023 sheet: 0.05 (1.11), residues: 25 loop : -0.15 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 142 TYR 0.025 0.002 TYR w 129 PHE 0.032 0.002 PHE r 122 TRP 0.021 0.002 TRP l 144 HIS 0.009 0.002 HIS d 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (40635) covalent geometry : angle 0.66232 / 0.34 (54838) SS BOND : bond 0.00686 / 0.40 ( 8) SS BOND : angle 1.90233 / 1.22 ( 16) hydrogen bonds : bond 0.06891 / 4.66 ( 2342) hydrogen bonds : angle 4.49909 / 3.28 ( 6774) Misc. bond : bond 0.00050 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 719 time to evaluate : 1.488 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: Q 58 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8169 (t) REVERT: W 85 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: X 80 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8748 (ttmt) REVERT: a 72 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8501 (ttm170) REVERT: a 163 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8662 (mtp180) REVERT: h 80 LYS cc_start: 0.7567 (tttt) cc_final: 0.7253 (tttm) REVERT: i 215 MET cc_start: 0.9267 (tpt) cc_final: 0.8984 (tpt) REVERT: j 5 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8696 (tt) REVERT: j 44 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7028 (tpp) REVERT: l 514 LYS cc_start: 0.8599 (tttt) cc_final: 0.8037 (tttt) REVERT: l 544 MET cc_start: 0.9026 (mmp) cc_final: 0.8797 (mmm) REVERT: m 1 MET cc_start: 0.2830 (mtt) cc_final: 0.2275 (mtp) REVERT: p 62 GLN cc_start: 0.7949 (tm130) cc_final: 0.6928 (mm-40) REVERT: p 66 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: p 95 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: p 124 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: p 138 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8091 (mmmt) REVERT: r 19 LYS cc_start: 0.8557 (mtmm) cc_final: 0.7927 (mppt) REVERT: r 114 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: s 202 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: u 38 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8130 (ttmm) REVERT: v 91 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: w 80 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8088 (mptm) REVERT: w 295 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8112 (ttt90) REVERT: w 333 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8240 (mt-10) outliers start: 84 outliers final: 29 residues processed: 757 average time/residue: 0.8860 time to fit residues: 797.0270 Evaluate side-chains 747 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 700 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain X residue 80 LYS Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain l residue 316 THR Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 55 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain p residue 95 GLU Chi-restraints excluded: chain p residue 124 GLN Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 254 LEU Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain w residue 80 LYS Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 295 ARG Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 125 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 367 optimal weight: 0.9990 chunk 313 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 327 optimal weight: 0.9980 chunk 374 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN h 21 GLN ** l 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 287 HIS u 64 ASN u 95 GLN u 143 HIS v 85 HIS v 110 GLN w 124 ASN ** w 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.124585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.103775 restraints weight = 42780.920| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.05 r_work: 0.2906 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 40646 Z= 0.116 Angle : 0.531 8.829 54854 Z= 0.272 Chirality : 0.040 0.187 5931 Planarity : 0.004 0.067 6680 Dihedral : 14.460 156.638 6326 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.96 % Rotamer: Outliers : 1.21 % Allowed : 10.18 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.10 (0.12), residues: 4667 helix: 2.20 (0.09), residues: 3011 sheet: 0.22 (1.08), residues: 25 loop : -0.10 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 43 TYR 0.022 0.001 TYR l 422 PHE 0.032 0.001 PHE i 292 TRP 0.022 0.001 TRP l 144 HIS 0.006 0.001 HIS i 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (40635) covalent geometry : angle 0.53036 / 0.27 (54838) SS BOND : bond 0.00398 / 0.26 ( 8) SS BOND : angle 1.47553 / 0.93 ( 16) hydrogen bonds : bond 0.04881 / 3.30 ( 2342) hydrogen bonds : angle 4.19398 / 3.07 ( 6774) Misc. bond : bond 0.00017 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 751 time to evaluate : 1.123 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: Q 58 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8164 (t) REVERT: W 121 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7245 (ttp) REVERT: a 163 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8509 (mtp180) REVERT: h 80 LYS cc_start: 0.7515 (tttt) cc_final: 0.7224 (tttm) REVERT: i 215 MET cc_start: 0.9182 (tpt) cc_final: 0.8881 (tpt) REVERT: j 5 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (tt) REVERT: j 44 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7019 (tpp) REVERT: k 6 MET cc_start: 0.8309 (mtt) cc_final: 0.8108 (mtt) REVERT: l 140 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9029 (tt) REVERT: l 514 LYS cc_start: 0.8537 (tttt) cc_final: 0.8012 (tttt) REVERT: l 544 MET cc_start: 0.8997 (mmp) cc_final: 0.8793 (tpt) REVERT: m 100 GLU cc_start: 0.8056 (tp30) cc_final: 0.7791 (tp30) REVERT: p 95 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: p 138 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7996 (mmmt) REVERT: r 19 LYS cc_start: 0.8463 (mtmm) cc_final: 0.7838 (mppt) REVERT: r 114 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: s 202 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: v 106 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7833 (ptm-80) REVERT: v 110 GLN cc_start: 0.7791 (mt0) cc_final: 0.7576 (mt0) REVERT: w 295 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8110 (ttt90) REVERT: w 333 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8106 (mt-10) outliers start: 50 outliers final: 12 residues processed: 773 average time/residue: 0.8335 time to fit residues: 765.8041 Evaluate side-chains 744 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 719 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 55 MET Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 95 GLU Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain v residue 106 ARG Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain w residue 295 ARG Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 111 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 427 optimal weight: 0.0470 chunk 216 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN Y 57 GLN c 127 ASN h 21 GLN ** l 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 287 HIS u 143 HIS v 85 HIS w 124 ASN w 202 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.099751 restraints weight = 42621.770| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.06 r_work: 0.2846 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 40646 Z= 0.174 Angle : 0.603 9.581 54854 Z= 0.309 Chirality : 0.044 0.202 5931 Planarity : 0.005 0.066 6680 Dihedral : 14.218 156.140 6326 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 1.79 % Allowed : 10.52 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.99 (0.12), residues: 4667 helix: 2.09 (0.09), residues: 3012 sheet: 0.24 (1.11), residues: 25 loop : -0.10 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 43 TYR 0.023 0.002 TYR w 129 PHE 0.029 0.002 PHE r 122 TRP 0.020 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (40635) covalent geometry : angle 0.60266 / 0.31 (54838) SS BOND : bond 0.00504 / 0.32 ( 8) SS BOND : angle 1.65842 / 1.06 ( 16) hydrogen bonds : bond 0.06040 / 4.09 ( 2342) hydrogen bonds : angle 4.30898 / 3.14 ( 6774) Misc. bond : bond 0.00063 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 726 time to evaluate : 1.525 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: Q 58 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8172 (t) REVERT: W 121 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7370 (ttp) REVERT: a 72 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8237 (ttt180) REVERT: a 163 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8610 (mtp180) REVERT: i 215 MET cc_start: 0.9248 (tpt) cc_final: 0.8956 (tpt) REVERT: j 5 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8673 (tt) REVERT: j 44 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.6971 (tpp) REVERT: k 6 MET cc_start: 0.8487 (mtt) cc_final: 0.8275 (mtt) REVERT: l 514 LYS cc_start: 0.8583 (tttt) cc_final: 0.8029 (tttt) REVERT: l 544 MET cc_start: 0.8997 (mmp) cc_final: 0.8796 (tpt) REVERT: m 100 GLU cc_start: 0.8178 (tp30) cc_final: 0.7923 (tp30) REVERT: m 135 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7354 (t80) REVERT: o 5 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7979 (tttm) REVERT: p 66 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: p 95 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: p 138 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8023 (mmmt) REVERT: r 19 LYS cc_start: 0.8509 (mtmm) cc_final: 0.7874 (mppt) REVERT: r 114 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: s 202 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: u 38 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8196 (ttmm) REVERT: w 80 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8038 (mptm) REVERT: w 295 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8162 (ttt90) REVERT: w 333 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8192 (mt-10) outliers start: 74 outliers final: 25 residues processed: 761 average time/residue: 0.8763 time to fit residues: 791.2003 Evaluate side-chains 745 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 703 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain p residue 95 GLU Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 254 LEU Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain w residue 80 LYS Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 295 ARG Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 199 optimal weight: 4.9990 chunk 320 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 301 optimal weight: 4.9990 chunk 331 optimal weight: 2.9990 chunk 424 optimal weight: 10.0000 chunk 283 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN c 127 ASN d 131 GLN e 65 ASN h 21 GLN ** l 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 12 HIS s 287 HIS u 95 GLN u 143 HIS v 85 HIS w 37 GLN w 124 ASN w 202 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.102585 restraints weight = 42830.770| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.06 r_work: 0.2887 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40646 Z= 0.128 Angle : 0.545 9.473 54854 Z= 0.278 Chirality : 0.041 0.211 5931 Planarity : 0.004 0.064 6680 Dihedral : 13.610 151.986 6326 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.83 % Rotamer: Outliers : 1.67 % Allowed : 11.08 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.15 (0.12), residues: 4667 helix: 2.23 (0.09), residues: 3011 sheet: 0.29 (1.10), residues: 25 loop : -0.05 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 43 TYR 0.020 0.001 TYR l 422 PHE 0.030 0.001 PHE i 292 TRP 0.021 0.001 TRP l 144 HIS 0.006 0.001 HIS i 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (40635) covalent geometry : angle 0.54387 / 0.28 (54838) SS BOND : bond 0.00461 / 0.29 ( 8) SS BOND : angle 1.74460 / 1.03 ( 16) hydrogen bonds : bond 0.05135 / 3.47 ( 2342) hydrogen bonds : angle 4.17949 / 3.05 ( 6774) Misc. bond : bond 0.00023 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 728 time to evaluate : 1.784 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: Q 58 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8164 (t) REVERT: a 163 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8542 (mtp180) REVERT: d 73 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8250 (p0) REVERT: i 215 MET cc_start: 0.9221 (tpt) cc_final: 0.8968 (tpt) REVERT: i 294 MET cc_start: 0.9150 (mmm) cc_final: 0.8903 (tpp) REVERT: j 5 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8681 (tt) REVERT: j 44 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7011 (tpp) REVERT: l 514 LYS cc_start: 0.8571 (tttt) cc_final: 0.8039 (tttt) REVERT: m 135 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7106 (t80) REVERT: p 66 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: p 95 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: p 138 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7952 (mmmt) REVERT: r 19 LYS cc_start: 0.8459 (mtmm) cc_final: 0.7849 (mppt) REVERT: r 114 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: s 202 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: s 227 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: w 72 ARG cc_start: 0.7221 (tpm170) cc_final: 0.7012 (tpp-160) REVERT: w 288 ASP cc_start: 0.7517 (m-30) cc_final: 0.7152 (t0) REVERT: w 295 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8166 (ttt90) REVERT: w 333 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8134 (mt-10) outliers start: 69 outliers final: 22 residues processed: 764 average time/residue: 0.8268 time to fit residues: 751.2828 Evaluate side-chains 749 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 713 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain p residue 95 GLU Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 295 ARG Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 169 optimal weight: 4.9990 chunk 421 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 374 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 361 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN Y 57 GLN c 127 ASN l 328 HIS ** l 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 287 HIS u 95 GLN u 143 HIS v 85 HIS v 110 GLN w 149 HIS w 202 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.117915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.096899 restraints weight = 42649.432| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.04 r_work: 0.2796 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 40646 Z= 0.255 Angle : 0.705 11.323 54854 Z= 0.362 Chirality : 0.049 0.285 5931 Planarity : 0.006 0.069 6680 Dihedral : 14.182 154.867 6326 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 2.11 % Allowed : 11.08 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.71 (0.12), residues: 4667 helix: 1.85 (0.09), residues: 3008 sheet: -0.02 (1.11), residues: 25 loop : -0.13 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG w 293 TYR 0.027 0.002 TYR w 129 PHE 0.033 0.003 PHE r 122 TRP 0.020 0.002 TRP l 144 HIS 0.009 0.002 HIS d 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.26 (40635) covalent geometry : angle 0.70408 / 0.36 (54838) SS BOND : bond 0.00680 / 0.41 ( 8) SS BOND : angle 2.08855 / 1.29 ( 16) hydrogen bonds : bond 0.07357 / 4.97 ( 2342) hydrogen bonds : angle 4.53032 / 3.29 ( 6774) Misc. bond : bond 0.00035 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 718 time to evaluate : 1.618 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: W 121 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7408 (ttp) REVERT: X 80 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8781 (ttmt) REVERT: Y 52 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6866 (mmt180) REVERT: a 72 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8252 (ttt180) REVERT: a 163 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8655 (mtp180) REVERT: d 73 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8298 (p0) REVERT: e 115 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: i 215 MET cc_start: 0.9287 (tpt) cc_final: 0.8931 (tpt) REVERT: j 5 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8708 (tt) REVERT: j 44 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7015 (tpp) REVERT: k 6 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8267 (mtt) REVERT: l 267 MET cc_start: 0.8549 (mmm) cc_final: 0.8289 (mmm) REVERT: l 514 LYS cc_start: 0.8645 (tttt) cc_final: 0.8072 (tttt) REVERT: m 103 MET cc_start: 0.7431 (ttp) cc_final: 0.7170 (ttt) REVERT: m 135 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.7330 (t80) REVERT: o 5 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7998 (tttm) REVERT: p 66 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: p 95 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: p 138 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8100 (mmmt) REVERT: r 19 LYS cc_start: 0.8565 (mtmm) cc_final: 0.7925 (mppt) REVERT: r 114 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: u 38 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8218 (ttmm) REVERT: v 91 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: w 80 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8128 (mptm) REVERT: w 289 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6851 (ptt-90) REVERT: w 295 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8221 (ttt90) REVERT: w 333 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8257 (mt-10) outliers start: 87 outliers final: 31 residues processed: 761 average time/residue: 0.8477 time to fit residues: 764.9830 Evaluate side-chains 759 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 706 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 53 TYR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 80 LYS Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 4 MET Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain k residue 6 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 316 THR Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 124 THR Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain p residue 95 GLU Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 446 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 254 LEU Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain w residue 80 LYS Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 289 ARG Chi-restraints excluded: chain w residue 295 ARG Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 385 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 393 optimal weight: 1.9990 chunk 360 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 chunk 291 optimal weight: 0.8980 chunk 407 optimal weight: 3.9990 chunk 324 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 288 optimal weight: 8.9990 chunk 305 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN Y 57 GLN c 127 ASN d 54 GLN ** l 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 287 HIS u 95 GLN u 143 HIS v 85 HIS w 202 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.122793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.102025 restraints weight = 42655.982| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.04 r_work: 0.2880 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40646 Z= 0.125 Angle : 0.554 10.778 54854 Z= 0.283 Chirality : 0.040 0.209 5931 Planarity : 0.004 0.067 6680 Dihedral : 13.334 145.482 6326 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 1.28 % Allowed : 12.24 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.06 (0.12), residues: 4667 helix: 2.17 (0.09), residues: 3006 sheet: 0.21 (1.09), residues: 25 loop : -0.08 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 43 TYR 0.020 0.001 TYR l 422 PHE 0.030 0.001 PHE i 292 TRP 0.025 0.001 TRP l 144 HIS 0.006 0.001 HIS i 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (40635) covalent geometry : angle 0.55317 / 0.28 (54838) SS BOND : bond 0.00393 / 0.26 ( 8) SS BOND : angle 1.49816 / 0.94 ( 16) hydrogen bonds : bond 0.05173 / 3.50 ( 2342) hydrogen bonds : angle 4.22517 / 3.09 ( 6774) Misc. bond : bond 0.00019 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 725 time to evaluate : 1.207 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 72 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8754 (ttm170) REVERT: a 163 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8531 (mtp180) REVERT: i 215 MET cc_start: 0.9222 (tpt) cc_final: 0.8967 (tpt) REVERT: i 294 MET cc_start: 0.9108 (mmm) cc_final: 0.8848 (tpp) REVERT: j 5 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8638 (tt) REVERT: j 44 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.6985 (tpp) REVERT: l 514 LYS cc_start: 0.8602 (tttt) cc_final: 0.8051 (tttt) REVERT: m 135 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.7015 (t80) REVERT: p 66 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: p 95 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: p 138 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8007 (mmmt) REVERT: r 19 LYS cc_start: 0.8465 (mtmm) cc_final: 0.7848 (mppt) REVERT: r 114 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: w 72 ARG cc_start: 0.7213 (tpm170) cc_final: 0.6991 (tpp-160) REVERT: w 288 ASP cc_start: 0.7479 (m-30) cc_final: 0.7144 (t0) REVERT: w 295 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8149 (ttt90) REVERT: w 333 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8141 (mt-10) outliers start: 53 outliers final: 20 residues processed: 752 average time/residue: 0.8337 time to fit residues: 744.3034 Evaluate side-chains 744 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 713 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain p residue 95 GLU Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 295 ARG Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 340 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 435 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 239 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN Y 57 GLN b 83 HIS c 127 ASN d 134 GLN f 73 ASN l 518 GLN ** l 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 287 HIS u 143 HIS v 85 HIS w 202 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.101867 restraints weight = 42960.041| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.04 r_work: 0.2877 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40646 Z= 0.132 Angle : 0.561 10.493 54854 Z= 0.286 Chirality : 0.041 0.243 5931 Planarity : 0.004 0.066 6680 Dihedral : 12.856 140.684 6326 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 1.28 % Allowed : 12.41 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.17 (0.12), residues: 4667 helix: 2.24 (0.09), residues: 3001 sheet: 0.21 (1.09), residues: 25 loop : -0.03 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 43 TYR 0.020 0.001 TYR l 422 PHE 0.030 0.001 PHE i 292 TRP 0.020 0.001 TRP l 144 HIS 0.006 0.001 HIS i 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (40635) covalent geometry : angle 0.56012 / 0.29 (54838) SS BOND : bond 0.00402 / 0.27 ( 8) SS BOND : angle 1.52690 / 0.96 ( 16) hydrogen bonds : bond 0.05240 / 3.54 ( 2342) hydrogen bonds : angle 4.18435 / 3.06 ( 6774) Misc. bond : bond 0.00023 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 715 time to evaluate : 1.766 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 72 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8202 (ttt180) REVERT: a 163 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8529 (mtp180) REVERT: i 215 MET cc_start: 0.9231 (tpt) cc_final: 0.8948 (tpt) REVERT: i 294 MET cc_start: 0.9133 (mmm) cc_final: 0.8917 (tpp) REVERT: j 5 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8669 (tt) REVERT: j 44 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7012 (tpp) REVERT: k 6 MET cc_start: 0.8334 (mtt) cc_final: 0.8099 (mtt) REVERT: l 514 LYS cc_start: 0.8593 (tttt) cc_final: 0.8066 (tttt) REVERT: m 100 GLU cc_start: 0.8129 (tp30) cc_final: 0.7810 (tp30) REVERT: m 135 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7064 (t80) REVERT: o 5 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7968 (tttm) REVERT: p 66 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: p 138 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8001 (mmmt) REVERT: r 19 LYS cc_start: 0.8474 (mtmm) cc_final: 0.7858 (mppt) REVERT: r 114 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: s 174 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8740 (ttm) REVERT: w 72 ARG cc_start: 0.7217 (tpm170) cc_final: 0.6993 (tpp-160) REVERT: w 288 ASP cc_start: 0.7440 (m-30) cc_final: 0.7091 (t0) REVERT: w 295 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8198 (ttt90) REVERT: w 333 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8137 (mt-10) outliers start: 53 outliers final: 24 residues processed: 740 average time/residue: 0.8885 time to fit residues: 777.9234 Evaluate side-chains 741 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 705 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 254 LEU Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 295 ARG Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 120 optimal weight: 0.0980 chunk 176 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 chunk 347 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 chunk 286 optimal weight: 8.9990 chunk 137 optimal weight: 0.0970 chunk 381 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN Y 57 GLN c 127 ASN f 73 ASN ** l 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 287 HIS u 143 HIS v 85 HIS v 110 GLN w 202 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.123227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.102894 restraints weight = 42848.624| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 0.94 r_work: 0.2892 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40646 Z= 0.127 Angle : 0.555 10.511 54854 Z= 0.283 Chirality : 0.040 0.227 5931 Planarity : 0.004 0.066 6680 Dihedral : 12.589 139.402 6326 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 1.09 % Allowed : 12.75 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.22 (0.12), residues: 4667 helix: 2.28 (0.09), residues: 3001 sheet: 0.20 (1.08), residues: 25 loop : 0.00 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 43 TYR 0.020 0.001 TYR l 422 PHE 0.030 0.001 PHE i 292 TRP 0.022 0.001 TRP l 144 HIS 0.006 0.001 HIS i 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (40635) covalent geometry : angle 0.55460 / 0.28 (54838) SS BOND : bond 0.00400 / 0.26 ( 8) SS BOND : angle 1.84925 / 1.05 ( 16) hydrogen bonds : bond 0.05063 / 3.42 ( 2342) hydrogen bonds : angle 4.14906 / 3.03 ( 6774) Misc. bond : bond 0.00021 / 0.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 716 time to evaluate : 1.641 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 72 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8754 (ttm170) REVERT: a 163 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8536 (mtp85) REVERT: h 80 LYS cc_start: 0.7586 (tttt) cc_final: 0.7309 (tttm) REVERT: i 215 MET cc_start: 0.9213 (tpt) cc_final: 0.8938 (tpt) REVERT: i 294 MET cc_start: 0.9090 (mmm) cc_final: 0.8865 (tpp) REVERT: j 5 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8666 (tt) REVERT: j 44 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: k 6 MET cc_start: 0.8313 (mtt) cc_final: 0.8089 (mtt) REVERT: l 514 LYS cc_start: 0.8584 (tttt) cc_final: 0.8077 (tttt) REVERT: m 100 GLU cc_start: 0.8074 (tp30) cc_final: 0.7830 (tp30) REVERT: m 135 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7058 (t80) REVERT: o 5 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7966 (tttm) REVERT: p 66 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7663 (mp10) REVERT: p 138 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7989 (mmmt) REVERT: r 19 LYS cc_start: 0.8470 (mtmm) cc_final: 0.7865 (mppt) REVERT: r 114 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: s 174 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8735 (ttm) REVERT: w 72 ARG cc_start: 0.7227 (tpm170) cc_final: 0.7018 (tpp-160) REVERT: w 288 ASP cc_start: 0.7397 (m-30) cc_final: 0.7069 (t0) REVERT: w 295 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8196 (ttt90) REVERT: w 333 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8113 (mt-10) outliers start: 45 outliers final: 24 residues processed: 737 average time/residue: 0.9026 time to fit residues: 786.0271 Evaluate side-chains 732 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 696 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 53 TYR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 254 LEU Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain w residue 248 GLU Chi-restraints excluded: chain w residue 295 ARG Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 412 optimal weight: 7.9990 chunk 383 optimal weight: 0.9990 chunk 453 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 439 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 286 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 389 optimal weight: 5.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN Y 57 GLN c 127 ASN f 73 ASN l 479 ASN ** l 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 287 HIS u 143 HIS v 85 HIS w 132 GLN w 202 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.123440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.102701 restraints weight = 42874.312| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.04 r_work: 0.2890 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40646 Z= 0.127 Angle : 0.555 10.463 54854 Z= 0.283 Chirality : 0.040 0.222 5931 Planarity : 0.004 0.064 6680 Dihedral : 12.326 138.461 6326 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 1.12 % Allowed : 12.95 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.25 (0.12), residues: 4667 helix: 2.30 (0.09), residues: 3000 sheet: 0.24 (1.08), residues: 25 loop : 0.02 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 43 TYR 0.020 0.001 TYR l 422 PHE 0.030 0.001 PHE i 292 TRP 0.021 0.001 TRP l 144 HIS 0.006 0.001 HIS i 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (40635) covalent geometry : angle 0.55444 / 0.28 (54838) SS BOND : bond 0.00401 / 0.26 ( 8) SS BOND : angle 1.84224 / 1.05 ( 16) hydrogen bonds : bond 0.05044 / 3.41 ( 2342) hydrogen bonds : angle 4.13664 / 3.02 ( 6774) Misc. bond : bond 0.00021 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20176.98 seconds wall clock time: 342 minutes 54.37 seconds (20574.37 seconds total)