Starting phenix.real_space_refine on Sat Mar 7 08:14:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vyg_32204/03_2026/7vyg_32204.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vyg_32204/03_2026/7vyg_32204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vyg_32204/03_2026/7vyg_32204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vyg_32204/03_2026/7vyg_32204.map" model { file = "/net/cci-nas-00/data/ceres_data/7vyg_32204/03_2026/7vyg_32204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vyg_32204/03_2026/7vyg_32204.cif" } resolution = 2.9 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= 0.006 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 35 5.49 5 S 293 5.16 5 C 26059 2.51 5 N 6282 2.21 5 O 6970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39639 Number of models: 1 Model: "" Number of chains: 46 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: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 699 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 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: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} 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: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4816 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 28, 'TRANS': 577} Chain: "m" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1292 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 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: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1530 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2502 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2583 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 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: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 156 Unusual residues: {'PEE': 2, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "l" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 335 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "m" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 95 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "n" 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: "r" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 202 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 8.33, per 1000 atoms: 0.21 Number of scatterers: 39639 At special positions: 0 Unit cell: (180.466, 195.504, 137.498, 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 35 15.00 O 6970 8.00 N 6282 7.00 C 26059 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=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 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=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8954 Finding SS restraints... Secondary structure from input PDB file: 219 helices and 5 sheets defined 69.5% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 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: 3.522A 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 31 removed outlier: 3.747A 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 55 Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'U' and resid 4 through 16 Processing helix chain 'U' and resid 16 through 32 Processing helix chain 'U' and resid 33 through 36 removed outlier: 3.617A pdb=" N SER U 36 " --> pdb=" O PRO U 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 33 through 36' Processing helix chain 'U' and resid 38 through 49 removed outlier: 3.530A pdb=" N THR U 49 " --> pdb=" O ILE U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 78 through 83 removed outlier: 3.647A pdb=" N ASN U 83 " --> pdb=" O GLU U 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 12 removed outlier: 4.048A pdb=" N ILE V 12 " --> pdb=" O LYS V 8 " (cutoff:3.500A) 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: 3.985A 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 129 through 143 removed outlier: 5.766A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 88 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 153 Processing helix chain 'Y' and resid 51 through 76 removed outlier: 3.837A 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 removed outlier: 3.673A pdb=" N LEU Y 97 " --> pdb=" O THR Y 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 22 removed outlier: 3.740A pdb=" N GLN Z 21 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 3.675A 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: 3.949A pdb=" N THR Z 31 " --> pdb=" O THR Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 50 Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' 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 removed outlier: 3.501A pdb=" N ARG a 65 " --> pdb=" O GLY a 61 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR a 78 " --> pdb=" O TYR a 74 " (cutoff:3.500A) Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 108 through 113 removed outlier: 3.732A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) removed outlier: 3.791A 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: 4.088A 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 69 through 74 Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'c' and resid 33 through 37 removed outlier: 3.505A pdb=" N PHE c 37 " --> pdb=" O LYS c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 55 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 41 Processing helix chain 'd' and resid 41 through 58 removed outlier: 3.611A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 77 Processing helix chain 'd' and resid 81 through 118 removed outlier: 3.841A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 125 removed outlier: 4.039A pdb=" N CYS d 125 " --> pdb=" O TYR d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 144 removed outlier: 3.668A pdb=" N LEU d 129 " --> pdb=" O CYS d 125 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 175 Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.514A pdb=" N LYS e 69 " --> pdb=" O ASN e 65 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN e 70 " --> pdb=" O LEU e 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 65 through 70' Processing helix chain 'e' and resid 79 through 96 Processing helix chain 'e' and resid 99 through 108 removed outlier: 3.546A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 132 removed outlier: 3.634A pdb=" N ALA e 118 " --> pdb=" O MET e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 143 through 147 removed outlier: 3.601A pdb=" N LYS e 146 " --> pdb=" O ASP e 143 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 73 Processing helix chain 'g' and resid 18 through 23 removed outlier: 3.560A pdb=" N LEU g 23 " --> pdb=" O ALA g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 51 Processing helix chain 'g' and resid 59 through 99 removed outlier: 3.824A 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 'h' and resid 5 through 11 Processing helix chain 'h' and resid 15 through 19 removed outlier: 3.727A pdb=" N MET h 18 " --> pdb=" O ASP h 15 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR h 19 " --> pdb=" O ARG h 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 15 through 19' Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 44 Processing helix chain 'h' and resid 48 through 56 removed outlier: 3.939A 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 removed outlier: 3.607A pdb=" N GLU h 89 " --> pdb=" O LYS h 85 " (cutoff:3.500A) 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 44 Proline residue: i 42 - end of helix 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: 4.321A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE i 122 " --> pdb=" O VAL i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 133 Processing helix chain 'i' and resid 135 through 145 removed outlier: 3.607A pdb=" N GLN i 144 " --> pdb=" O SER i 140 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE i 145 " --> pdb=" O VAL i 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 150 through 170 removed outlier: 3.856A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 174 through 194 removed outlier: 3.949A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU i 194 " --> pdb=" O MET i 190 " (cutoff:3.500A) Processing helix chain 'i' and resid 197 through 222 removed outlier: 3.534A 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 271 removed outlier: 4.470A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 4.006A pdb=" N LEU i 287 " --> pdb=" O ALA i 283 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU i 296 " --> pdb=" O PHE i 292 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 3.714A 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 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 55 through 73 removed outlier: 3.916A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 79 Processing helix chain 'j' and resid 83 through 108 Processing helix chain 'k' and resid 2 through 21 Processing helix chain 'k' and resid 25 through 52 removed outlier: 3.817A 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 removed outlier: 3.628A pdb=" N GLU k 70 " --> pdb=" O PHE k 66 " (cutoff:3.500A) Processing helix chain 'k' and resid 89 through 93 Processing helix chain 'l' and resid 2 through 14 removed outlier: 4.471A pdb=" N SER l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 22 Processing helix chain 'l' and resid 31 through 58 removed outlier: 4.268A 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: 3.846A 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 removed outlier: 3.512A pdb=" N GLY l 156 " --> pdb=" O PHE l 152 " (cutoff:3.500A) Processing helix chain 'l' and resid 161 through 194 removed outlier: 3.821A pdb=" N GLY l 178 " --> pdb=" O TYR l 174 " (cutoff:3.500A) removed outlier: 4.011A 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 225 removed outlier: 4.322A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.990A pdb=" N HIS l 230 " --> pdb=" O PHE l 227 " (cutoff:3.500A) Processing helix chain 'l' and resid 231 through 236 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 271 through 293 removed outlier: 3.591A pdb=" N ALA l 289 " --> pdb=" O THR l 285 " (cutoff:3.500A) removed outlier: 3.676A 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: 4.116A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.881A 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 391 through 401 Processing helix chain 'l' and resid 405 through 432 removed outlier: 3.690A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU l 432 " --> pdb=" O PHE l 428 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 470 removed outlier: 3.702A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.466A 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 removed outlier: 3.525A pdb=" N HIS l 534 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 535 through 548 removed outlier: 3.610A pdb=" N GLN l 546 " --> pdb=" O LEU l 542 " (cutoff:3.500A) Processing helix chain 'l' and resid 556 through 562 removed outlier: 3.719A pdb=" N LEU l 562 " --> pdb=" O LEU l 558 " (cutoff:3.500A) Processing helix chain 'l' and resid 562 through 579 removed outlier: 3.547A pdb=" N THR l 566 " --> pdb=" O LEU l 562 " (cutoff:3.500A) Processing helix chain 'l' and resid 583 through 603 removed outlier: 3.709A pdb=" N TYR l 587 " --> pdb=" O LEU l 583 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU l 589 " --> pdb=" O LYS l 585 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 22 Processing helix chain 'm' and resid 25 through 47 removed outlier: 3.513A pdb=" N PHE m 47 " --> pdb=" O ILE m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 75 removed outlier: 4.562A pdb=" N GLY m 62 " --> pdb=" O LEU m 58 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA m 73 " --> pdb=" O GLY m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 110 Processing helix chain 'm' and resid 137 through 145 Processing helix chain 'm' and resid 145 through 150 Processing helix chain 'm' and resid 150 through 172 Processing helix chain 'n' and resid 4 through 12 removed outlier: 4.779A pdb=" N ASP n 10 " --> pdb=" O GLN n 6 " (cutoff:3.500A) Processing helix chain 'n' and resid 15 through 33 Processing helix chain 'o' and resid 19 through 24 removed outlier: 3.521A pdb=" N GLU o 22 " --> pdb=" O ASP o 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP o 24 " --> pdb=" O ALA o 21 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 52 removed outlier: 3.715A 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 removed outlier: 3.504A pdb=" N GLU o 118 " --> pdb=" O LYS o 114 " (cutoff:3.500A) 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 100 through 107 removed outlier: 3.639A pdb=" N TRP p 107 " --> pdb=" O LEU p 104 " (cutoff:3.500A) Processing helix chain 'p' and resid 108 through 114 removed outlier: 3.641A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 131 removed outlier: 3.571A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) Processing helix chain 'p' and resid 132 through 143 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: 4.252A 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: 3.665A 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: 4.110A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 88 through 111 removed outlier: 3.571A 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: 3.885A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 172 removed outlier: 3.811A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.554A pdb=" N VAL r 162 " --> pdb=" O LEU r 158 " (cutoff:3.500A) Processing helix chain 'r' and resid 175 through 182 Processing helix chain 'r' and resid 189 through 205 removed outlier: 4.127A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 4.098A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL r 221 " --> pdb=" O PRO r 217 " (cutoff:3.500A) Processing helix chain 'r' and resid 224 through 234 Processing helix chain 'r' and resid 236 through 251 removed outlier: 4.103A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU r 250 " --> pdb=" O ILE r 246 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN r 251 " --> pdb=" O THR r 247 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 258 removed outlier: 3.518A pdb=" N ALA r 258 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 258 through 278 removed outlier: 4.225A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 281 through 304 removed outlier: 4.134A pdb=" N LEU r 296 " --> pdb=" O SER r 292 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL r 297 " --> pdb=" O HIS r 293 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN r 304 " --> pdb=" O ALA r 300 " (cutoff:3.500A) Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.506A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (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: 4.070A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA r 404 " --> pdb=" O MET r 400 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR r 414 " --> pdb=" O MET r 410 " (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 removed outlier: 3.633A pdb=" N LEU r 455 " --> pdb=" O LYS r 452 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.699A 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 123 removed outlier: 3.501A pdb=" N PHE s 104 " --> pdb=" O LEU s 100 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 5.002A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 4.167A 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 removed outlier: 3.696A pdb=" N MET s 184 " --> pdb=" O PRO s 180 " (cutoff:3.500A) Processing helix chain 's' and resid 203 through 208 removed outlier: 3.613A pdb=" N VAL s 208 " --> pdb=" O GLU s 204 " (cutoff:3.500A) Processing helix chain 's' and resid 209 through 213 removed outlier: 3.987A pdb=" N ASN s 212 " --> pdb=" O SER s 209 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL s 213 " --> pdb=" O GLY s 210 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 209 through 213' Processing helix chain 's' and resid 216 through 243 removed outlier: 3.789A pdb=" N PHE s 220 " --> pdb=" O ALA s 216 " (cutoff:3.500A) Processing helix chain 's' and resid 252 through 275 removed outlier: 3.556A pdb=" N ALA s 275 " --> pdb=" O LEU s 271 " (cutoff:3.500A) Processing helix chain 's' and resid 281 through 292 removed outlier: 3.698A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 292 through 312 removed outlier: 3.751A 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: 5.036A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 51 removed outlier: 3.526A pdb=" N ASN u 40 " --> pdb=" O CYS u 36 " (cutoff:3.500A) Processing helix chain 'u' and resid 56 through 78 removed outlier: 3.563A pdb=" N GLY u 60 " --> pdb=" O CYS u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 79 through 92 removed outlier: 3.713A pdb=" N CYS u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 100 through 116 removed outlier: 4.037A pdb=" N GLN u 104 " --> pdb=" O CYS u 100 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 11 Processing helix chain 'v' and resid 12 through 16 removed outlier: 3.521A pdb=" N LYS v 15 " --> pdb=" O ASP v 12 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU v 16 " --> pdb=" O ALA v 13 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'v' and resid 80 through 124 removed outlier: 3.598A pdb=" N GLN v 84 " --> pdb=" O CYS v 80 " (cutoff:3.500A) 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: 3.723A 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: 3.963A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 195 removed outlier: 3.714A pdb=" N VAL w 193 " --> pdb=" O GLU w 189 " (cutoff:3.500A) 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: 3.921A 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 244 removed outlier: 3.696A pdb=" N LEU w 234 " --> pdb=" O THR w 230 " (cutoff:3.500A) Processing helix chain 'w' and resid 244 through 251 Processing helix chain 'w' and resid 261 through 264 Processing helix chain 'w' and resid 265 through 275 removed outlier: 3.826A pdb=" N VAL w 269 " --> pdb=" O ASP w 265 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR w 275 " --> pdb=" O GLU w 271 " (cutoff:3.500A) Processing helix chain 'w' and resid 287 through 299 removed outlier: 3.562A pdb=" N GLN w 299 " --> pdb=" O ARG w 295 " (cutoff:3.500A) Processing helix chain 'w' and resid 300 through 305 Processing helix chain 'w' and resid 306 through 310 removed outlier: 3.875A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE w 310 " --> pdb=" O TYR w 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 310' Processing helix chain 'w' and resid 320 through 333 Processing helix chain 'w' and resid 344 through 348 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: 6.650A 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: 5.908A 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: 5.336A pdb=" N SER l 64 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE l 80 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP l 66 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU l 76 " --> pdb=" O TRP l 68 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR l 70 " --> pdb=" O VAL l 74 " (cutoff:3.500A) removed outlier: 6.400A 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 86 removed outlier: 6.412A pdb=" N ILE w 60 " --> pdb=" O LEU w 159 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR w 61 " --> pdb=" O VAL w 205 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL w 207 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP w 63 " --> pdb=" O VAL w 207 " (cutoff:3.500A) 2257 hydrogen bonds defined for protein. 6594 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: 6.66 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5978 1.31 - 1.44: 10999 1.44 - 1.58: 23022 1.58 - 1.71: 120 1.71 - 1.84: 529 Bond restraints: 40648 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C18 UQ s 402 " pdb=" C19 UQ s 402 " ideal model delta sigma weight residual 1.336 1.557 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CA7 CDL m 201 " pdb=" OA8 CDL m 201 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CB7 CDL m 201 " pdb=" OB8 CDL m 201 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.13e+02 bond pdb=" C13 UQ s 402 " pdb=" C14 UQ s 402 " ideal model delta sigma weight residual 1.335 1.547 -0.212 2.00e-02 2.50e+03 1.13e+02 ... (remaining 40643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 54186 3.40 - 6.79: 528 6.79 - 10.19: 95 10.19 - 13.59: 30 13.59 - 16.98: 10 Bond angle restraints: 54849 Sorted by residual: angle pdb=" C51 CDL m 201 " pdb=" CB5 CDL m 201 " pdb=" OB6 CDL m 201 " ideal model delta sigma weight residual 111.33 120.27 -8.94 1.32e+00 5.72e-01 4.58e+01 angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.25 -8.92 1.32e+00 5.72e-01 4.55e+01 angle pdb=" C51 CDL s 401 " pdb=" CB5 CDL s 401 " pdb=" OB6 CDL s 401 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.51e+01 angle pdb=" C11 CDL V 202 " pdb=" CA5 CDL V 202 " pdb=" OA6 CDL V 202 " ideal model delta sigma weight residual 111.33 120.18 -8.85 1.32e+00 5.72e-01 4.48e+01 angle pdb=" C11 CDL V 201 " pdb=" CA5 CDL V 201 " pdb=" OA6 CDL V 201 " ideal model delta sigma weight residual 111.33 120.16 -8.83 1.32e+00 5.72e-01 4.47e+01 ... (remaining 54844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 23824 34.83 - 69.66: 897 69.66 - 104.49: 77 104.49 - 139.32: 16 139.32 - 174.15: 25 Dihedral angle restraints: 24839 sinusoidal: 10978 harmonic: 13861 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 300.00 126.32 173.68 1 2.00e+01 2.50e-03 4.79e+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 -143.81 57.81 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CB CYS d 113 " pdb=" SG CYS d 113 " pdb=" SG CYS d 125 " pdb=" CB CYS d 125 " ideal model delta sinusoidal sigma weight residual -86.00 -132.91 46.91 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 24836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5382 0.072 - 0.145: 509 0.145 - 0.217: 22 0.217 - 0.289: 8 0.289 - 0.361: 9 Chirality restraints: 5930 Sorted by residual: chirality pdb=" CA TYR m 60 " pdb=" N TYR m 60 " pdb=" C TYR m 60 " pdb=" CB TYR m 60 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA LYS m 23 " pdb=" N LYS m 23 " pdb=" C LYS m 23 " pdb=" CB LYS m 23 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C6 PLX g 201 " pdb=" C7 PLX g 201 " pdb=" O6 PLX g 201 " pdb=" O7 PLX g 201 " both_signs ideal model delta sigma weight residual False 2.01 2.35 -0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 5927 not shown) Planarity restraints: 6675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.075 2.00e-02 2.50e+03 2.66e-01 8.86e+02 pdb=" C11 UQ s 402 " 0.098 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.253 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.468 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " -0.237 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.176 2.00e-02 2.50e+03 2.12e-01 5.64e+02 pdb=" C18 UQ s 402 " -0.114 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.347 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.042 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 402 " -0.105 2.00e-02 2.50e+03 1.63e-01 3.34e+02 pdb=" C13 UQ s 402 " 0.037 2.00e-02 2.50e+03 pdb=" C14 UQ s 402 " 0.297 2.00e-02 2.50e+03 pdb=" C15 UQ s 402 " -0.055 2.00e-02 2.50e+03 pdb=" C16 UQ s 402 " -0.174 2.00e-02 2.50e+03 ... (remaining 6672 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2918 2.74 - 3.28: 39045 3.28 - 3.82: 67247 3.82 - 4.36: 82483 4.36 - 4.90: 140937 Nonbonded interactions: 332630 Sorted by model distance: nonbonded pdb=" OH TYR n 26 " pdb=" NH2 ARG n 30 " model vdw 2.197 3.120 nonbonded pdb=" OG1 THR r 357 " pdb=" O1 CDL l 702 " model vdw 2.199 3.040 nonbonded pdb=" O ASP Y 76 " pdb=" OH TYR l 385 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR l 515 " pdb=" OE2 GLU p 70 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR w 118 " pdb=" O2' ADP w 401 " model vdw 2.218 3.040 ... (remaining 332625 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 31.610 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.008 0.245 40657 Z= 0.451 Angle : 0.879 16.983 54865 Z= 0.431 Chirality : 0.045 0.361 5930 Planarity : 0.007 0.266 6675 Dihedral : 18.318 174.148 15861 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 0.17 % Allowed : 0.39 % Favored : 99.44 % 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: 1.36 (0.12), residues: 4666 helix: 1.78 (0.10), residues: 2933 sheet: -1.01 (0.99), residues: 23 loop : -0.60 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 68 TYR 0.023 0.001 TYR s 282 PHE 0.029 0.002 PHE s 270 TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS S 27 Details of bonding type rmsd covalent geometry : bond 0.00789 (40648) covalent geometry : angle 0.87853 (54849) SS BOND : bond 0.00300 ( 8) SS BOND : angle 2.38252 ( 16) hydrogen bonds : bond 0.12525 ( 2257) hydrogen bonds : angle 5.48550 ( 6594) Misc. bond : bond 0.24495 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 787 time to evaluate : 1.540 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: d 73 ASP cc_start: 0.7906 (p0) cc_final: 0.7306 (p0) REVERT: f 53 PHE cc_start: 0.8492 (t80) cc_final: 0.8085 (t80) REVERT: h 18 MET cc_start: 0.8400 (ttt) cc_final: 0.8164 (ttt) REVERT: i 89 MET cc_start: 0.8320 (tpt) cc_final: 0.7587 (tpt) REVERT: k 97 GLN cc_start: 0.8469 (mp10) cc_final: 0.8236 (mp10) REVERT: l 163 ASP cc_start: 0.7798 (m-30) cc_final: 0.7575 (m-30) REVERT: r 401 MET cc_start: 0.8745 (ttp) cc_final: 0.8519 (ttm) REVERT: u 9 THR cc_start: 0.9131 (p) cc_final: 0.8870 (p) outliers start: 7 outliers final: 5 residues processed: 792 average time/residue: 0.7912 time to fit residues: 746.2528 Evaluate side-chains 660 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 655 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 TYR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain m residue 23 LYS Chi-restraints excluded: chain m residue 148 SER 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: 0.6980 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN b 89 HIS c 160 GLN ** h 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 150 ASN j 26 GLN l 351 ASN l 405 ASN m 46 ASN p 62 GLN r 51 ASN r 103 GLN u 64 ASN u 77 HIS v 47 ASN v 76 ASN w 202 HIS w 322 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.096541 restraints weight = 52147.878| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.24 r_work: 0.2876 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40657 Z= 0.133 Angle : 0.572 9.057 54865 Z= 0.287 Chirality : 0.041 0.298 5930 Planarity : 0.005 0.044 6675 Dihedral : 18.382 170.961 6639 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 1.70 % Allowed : 8.75 % Favored : 89.55 % 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: 1.76 (0.13), residues: 4666 helix: 2.08 (0.10), residues: 2952 sheet: -1.10 (0.98), residues: 23 loop : -0.44 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 173 TYR 0.028 0.001 TYR l 422 PHE 0.027 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS S 27 Details of bonding type rmsd covalent geometry : bond 0.00300 (40648) covalent geometry : angle 0.57105 (54849) SS BOND : bond 0.00297 ( 8) SS BOND : angle 2.32770 ( 16) hydrogen bonds : bond 0.04828 ( 2257) hydrogen bonds : angle 4.26759 ( 6594) Misc. bond : bond 0.00476 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 699 time to evaluate : 1.535 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 16 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8376 (mm-30) REVERT: U 41 TYR cc_start: 0.8871 (m-80) cc_final: 0.8569 (m-10) REVERT: V 50 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7406 (tp) REVERT: W 108 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: Y 76 ASP cc_start: 0.8464 (m-30) cc_final: 0.8141 (m-30) REVERT: Y 88 ASP cc_start: 0.8206 (t0) cc_final: 0.7971 (t70) REVERT: a 69 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8428 (pttt) REVERT: b 93 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8151 (mttp) REVERT: b 108 ASP cc_start: 0.8815 (m-30) cc_final: 0.8577 (m-30) REVERT: d 79 GLU cc_start: 0.7633 (tt0) cc_final: 0.7340 (tm-30) REVERT: d 172 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6753 (mt-10) REVERT: f 53 PHE cc_start: 0.8583 (t80) cc_final: 0.8105 (t80) REVERT: h 18 MET cc_start: 0.8904 (ttt) cc_final: 0.8673 (ttt) REVERT: i 245 MET cc_start: 0.9048 (tmm) cc_final: 0.8722 (ttp) REVERT: i 321 LYS cc_start: 0.7741 (tmmt) cc_final: 0.7246 (tmtm) REVERT: j 105 GLU cc_start: 0.8987 (tt0) cc_final: 0.8768 (tt0) REVERT: k 97 GLN cc_start: 0.8595 (mp10) cc_final: 0.8210 (mp10) REVERT: l 163 ASP cc_start: 0.8564 (m-30) cc_final: 0.8321 (m-30) REVERT: l 383 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8870 (tpt) REVERT: l 484 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8596 (tp) REVERT: m 98 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7274 (mmp) REVERT: m 138 GLU cc_start: 0.8506 (mp0) cc_final: 0.8234 (mt-10) REVERT: m 169 MET cc_start: 0.8899 (mmm) cc_final: 0.8569 (mtp) REVERT: n 30 ARG cc_start: 0.8433 (mtp180) cc_final: 0.8224 (ttt-90) REVERT: n 48 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7461 (mp0) REVERT: o 19 ASP cc_start: 0.8668 (t0) cc_final: 0.8260 (t0) REVERT: o 22 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: p 138 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7899 (tptt) REVERT: r 378 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: u 157 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7168 (m-30) REVERT: v 81 LYS cc_start: 0.8259 (mtpp) cc_final: 0.7868 (mmpt) outliers start: 70 outliers final: 25 residues processed: 728 average time/residue: 0.7982 time to fit residues: 692.4878 Evaluate side-chains 690 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 653 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 172 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 219 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 400 optimal weight: 0.7980 chunk 396 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 370 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 160 GLN j 26 GLN k 83 ASN r 44 GLN ** r 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN u 77 HIS v 76 ASN w 202 HIS w 286 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.094088 restraints weight = 51949.465| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.23 r_work: 0.2835 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40657 Z= 0.171 Angle : 0.587 8.667 54865 Z= 0.294 Chirality : 0.043 0.277 5930 Planarity : 0.005 0.048 6675 Dihedral : 17.331 177.394 6628 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 2.24 % Allowed : 10.54 % Favored : 87.22 % 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: 1.69 (0.12), residues: 4666 helix: 2.04 (0.09), residues: 2954 sheet: -1.36 (0.96), residues: 23 loop : -0.49 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 16 TYR 0.025 0.002 TYR l 587 PHE 0.028 0.002 PHE i 292 TRP 0.018 0.001 TRP u 86 HIS 0.009 0.001 HIS S 27 Details of bonding type rmsd covalent geometry : bond 0.00410 (40648) covalent geometry : angle 0.58561 (54849) SS BOND : bond 0.00316 ( 8) SS BOND : angle 2.37828 ( 16) hydrogen bonds : bond 0.05232 ( 2257) hydrogen bonds : angle 4.20077 ( 6594) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 678 time to evaluate : 1.578 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 16 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8421 (mm-30) REVERT: U 41 TYR cc_start: 0.8893 (m-80) cc_final: 0.8625 (m-10) REVERT: W 108 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: Y 76 ASP cc_start: 0.8573 (m-30) cc_final: 0.8212 (m-30) REVERT: Y 88 ASP cc_start: 0.8094 (t0) cc_final: 0.7849 (t70) REVERT: a 69 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8430 (pttt) REVERT: b 16 ARG cc_start: 0.8330 (mtm110) cc_final: 0.7969 (mtt-85) REVERT: b 93 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8132 (mttp) REVERT: c 99 LEU cc_start: 0.9480 (mt) cc_final: 0.9270 (mp) REVERT: d 32 TYR cc_start: 0.7785 (t80) cc_final: 0.7294 (m-80) REVERT: d 172 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: i 89 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8269 (tpt) REVERT: i 245 MET cc_start: 0.9093 (tmm) cc_final: 0.8752 (ttp) REVERT: i 321 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7245 (tmtm) REVERT: j 105 GLU cc_start: 0.9051 (tt0) cc_final: 0.8843 (tt0) REVERT: k 97 GLN cc_start: 0.8612 (mp10) cc_final: 0.8087 (mp10) REVERT: l 163 ASP cc_start: 0.8596 (m-30) cc_final: 0.8340 (m-30) REVERT: l 267 MET cc_start: 0.8991 (mtp) cc_final: 0.8760 (mmm) REVERT: l 383 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8924 (tpt) REVERT: l 484 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8602 (tp) REVERT: m 138 GLU cc_start: 0.8449 (mp0) cc_final: 0.8204 (mt-10) REVERT: m 169 MET cc_start: 0.8901 (mmm) cc_final: 0.8673 (mtp) REVERT: n 30 ARG cc_start: 0.8524 (mtp180) cc_final: 0.8291 (ttt-90) REVERT: r 378 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: s 227 GLU cc_start: 0.8429 (tp30) cc_final: 0.8193 (tm-30) REVERT: u 157 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7184 (m-30) REVERT: v 84 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8823 (tp-100) REVERT: v 103 GLU cc_start: 0.8504 (tp30) cc_final: 0.8136 (tp30) REVERT: w 45 LEU cc_start: 0.8234 (mp) cc_final: 0.7986 (pp) outliers start: 92 outliers final: 38 residues processed: 711 average time/residue: 0.8118 time to fit residues: 686.5959 Evaluate side-chains 697 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 647 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 41 VAL Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 172 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 84 GLN Chi-restraints excluded: chain v residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 385 optimal weight: 2.9990 chunk 365 optimal weight: 3.9990 chunk 377 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 0.0770 chunk 440 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 230 optimal weight: 0.6980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN j 26 GLN k 83 ASN l 405 ASN l 580 GLN r 44 GLN r 103 GLN r 304 GLN u 77 HIS v 44 GLN v 76 ASN v 84 GLN w 202 HIS w 286 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.095936 restraints weight = 52082.265| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.24 r_work: 0.2868 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40657 Z= 0.124 Angle : 0.537 9.154 54865 Z= 0.269 Chirality : 0.040 0.272 5930 Planarity : 0.004 0.044 6675 Dihedral : 16.473 178.222 6627 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 2.16 % Allowed : 11.76 % Favored : 86.08 % 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: 1.87 (0.13), residues: 4666 helix: 2.19 (0.09), residues: 2955 sheet: -1.29 (0.98), residues: 23 loop : -0.44 (0.16), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 173 TYR 0.022 0.001 TYR l 422 PHE 0.027 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS u 77 Details of bonding type rmsd covalent geometry : bond 0.00283 (40648) covalent geometry : angle 0.53580 (54849) SS BOND : bond 0.00356 ( 8) SS BOND : angle 1.96496 ( 16) hydrogen bonds : bond 0.04526 ( 2257) hydrogen bonds : angle 4.05585 ( 6594) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 681 time to evaluate : 1.667 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 16 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8430 (mm-30) REVERT: U 41 TYR cc_start: 0.8914 (m-80) cc_final: 0.8625 (m-10) REVERT: W 94 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: W 108 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: Y 88 ASP cc_start: 0.8085 (t0) cc_final: 0.7848 (t70) REVERT: a 71 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8948 (ttm) REVERT: b 93 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8109 (mttp) REVERT: b 122 GLU cc_start: 0.7423 (tp30) cc_final: 0.7187 (tt0) REVERT: d 32 TYR cc_start: 0.7730 (t80) cc_final: 0.7239 (m-80) REVERT: f 53 PHE cc_start: 0.8590 (t80) cc_final: 0.8165 (t80) REVERT: h 65 GLU cc_start: 0.8896 (tp30) cc_final: 0.8632 (tp30) REVERT: i 89 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8274 (tpt) REVERT: i 245 MET cc_start: 0.9088 (tmm) cc_final: 0.8761 (ttp) REVERT: i 321 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7196 (tmtm) REVERT: k 97 GLN cc_start: 0.8635 (mp10) cc_final: 0.8169 (mp10) REVERT: l 163 ASP cc_start: 0.8558 (m-30) cc_final: 0.8310 (m-30) REVERT: l 267 MET cc_start: 0.8919 (mtp) cc_final: 0.8676 (mmm) REVERT: l 484 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8572 (tp) REVERT: m 98 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7370 (mmp) REVERT: m 138 GLU cc_start: 0.8431 (mp0) cc_final: 0.8220 (mt-10) REVERT: m 169 MET cc_start: 0.8828 (mmm) cc_final: 0.8604 (mtp) REVERT: o 31 LYS cc_start: 0.8524 (mtpm) cc_final: 0.7857 (mtmt) REVERT: o 118 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: r 378 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: s 227 GLU cc_start: 0.8402 (tp30) cc_final: 0.8152 (tm-30) REVERT: u 157 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: v 15 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8332 (mtpp) REVERT: v 81 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7900 (mmpt) REVERT: v 103 GLU cc_start: 0.8509 (tp30) cc_final: 0.8199 (tp30) REVERT: w 45 LEU cc_start: 0.8089 (mp) cc_final: 0.7826 (pp) outliers start: 89 outliers final: 32 residues processed: 714 average time/residue: 0.8010 time to fit residues: 680.1640 Evaluate side-chains 690 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 646 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 231 ILE Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain u residue 165 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 171 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 220 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 440 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN j 26 GLN k 83 ASN p 62 GLN r 44 GLN r 103 GLN r 304 GLN s 258 ASN u 64 ASN u 77 HIS v 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.117273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.097684 restraints weight = 51818.687| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.23 r_work: 0.2899 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 40657 Z= 0.108 Angle : 0.514 7.991 54865 Z= 0.257 Chirality : 0.039 0.256 5930 Planarity : 0.004 0.046 6675 Dihedral : 15.620 173.263 6627 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.07 % Allowed : 12.61 % Favored : 85.33 % 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: 2.03 (0.13), residues: 4666 helix: 2.34 (0.09), residues: 2949 sheet: -1.24 (0.98), residues: 23 loop : -0.40 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 16 TYR 0.022 0.001 TYR l 422 PHE 0.027 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS u 77 Details of bonding type rmsd covalent geometry : bond 0.00236 (40648) covalent geometry : angle 0.51308 (54849) SS BOND : bond 0.00244 ( 8) SS BOND : angle 1.70764 ( 16) hydrogen bonds : bond 0.04123 ( 2257) hydrogen bonds : angle 3.94062 ( 6594) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 699 time to evaluate : 1.451 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: S 28 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8688 (mppt) REVERT: U 16 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8446 (mm-30) REVERT: U 41 TYR cc_start: 0.8874 (m-80) cc_final: 0.8560 (m-10) REVERT: V 50 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7389 (tp) REVERT: V 83 LYS cc_start: 0.7957 (mmpt) cc_final: 0.7524 (tptp) REVERT: W 94 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: W 108 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: Y 88 ASP cc_start: 0.8085 (t0) cc_final: 0.7873 (t70) REVERT: Y 94 ASP cc_start: 0.8040 (m-30) cc_final: 0.7643 (t0) REVERT: a 71 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8911 (ttm) REVERT: b 16 ARG cc_start: 0.8266 (mtm110) cc_final: 0.7934 (mtt-85) REVERT: b 35 LEU cc_start: 0.8454 (mt) cc_final: 0.8201 (mp) REVERT: b 93 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8049 (mttp) REVERT: b 108 ASP cc_start: 0.8799 (m-30) cc_final: 0.8583 (m-30) REVERT: c 63 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8256 (pp20) REVERT: d 32 TYR cc_start: 0.7669 (t80) cc_final: 0.7207 (m-80) REVERT: d 172 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: f 53 PHE cc_start: 0.8588 (t80) cc_final: 0.8190 (t80) REVERT: g 109 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8205 (mtmp) REVERT: i 89 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8399 (tpt) REVERT: i 321 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7251 (mmmt) REVERT: k 97 GLN cc_start: 0.8635 (mp10) cc_final: 0.8347 (mp10) REVERT: l 163 ASP cc_start: 0.8510 (m-30) cc_final: 0.8260 (m-30) REVERT: l 207 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5635 (pp20) REVERT: l 484 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8525 (tp) REVERT: l 580 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.6476 (mp10) REVERT: m 46 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8368 (t0) REVERT: m 98 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7377 (mmp) REVERT: o 31 LYS cc_start: 0.8482 (mtpm) cc_final: 0.7809 (mtmt) REVERT: o 118 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7109 (pt0) REVERT: r 378 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: r 453 MET cc_start: 0.8515 (mmp) cc_final: 0.8265 (mmt) REVERT: u 157 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: v 15 LYS cc_start: 0.8571 (mtpt) cc_final: 0.8314 (mtpp) REVERT: v 81 LYS cc_start: 0.8328 (mtpp) cc_final: 0.7940 (mmpt) REVERT: v 103 GLU cc_start: 0.8481 (tp30) cc_final: 0.8188 (tp30) REVERT: w 45 LEU cc_start: 0.8121 (mp) cc_final: 0.7771 (pp) REVERT: w 261 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6653 (ttm110) REVERT: w 267 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7148 (tp30) outliers start: 85 outliers final: 31 residues processed: 738 average time/residue: 0.7928 time to fit residues: 697.5368 Evaluate side-chains 715 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 664 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 172 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 47 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 207 GLU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 46 ASN Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 56 CYS Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain w residue 261 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 236 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN j 26 GLN k 83 ASN r 44 GLN r 51 ASN r 169 ASN r 304 GLN u 64 ASN u 77 HIS v 44 GLN v 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.097408 restraints weight = 52158.679| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.24 r_work: 0.2891 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40657 Z= 0.115 Angle : 0.524 8.917 54865 Z= 0.262 Chirality : 0.040 0.247 5930 Planarity : 0.004 0.046 6675 Dihedral : 15.249 169.290 6627 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.16 % Allowed : 13.36 % Favored : 84.48 % 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: 2.08 (0.13), residues: 4666 helix: 2.36 (0.09), residues: 2946 sheet: -1.17 (0.99), residues: 23 loop : -0.36 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 16 TYR 0.021 0.001 TYR l 422 PHE 0.027 0.001 PHE i 292 TRP 0.018 0.001 TRP u 86 HIS 0.007 0.001 HIS u 77 Details of bonding type rmsd covalent geometry : bond 0.00258 (40648) covalent geometry : angle 0.52348 (54849) SS BOND : bond 0.00246 ( 8) SS BOND : angle 1.70582 ( 16) hydrogen bonds : bond 0.04170 ( 2257) hydrogen bonds : angle 3.92715 ( 6594) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 682 time to evaluate : 1.523 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: S 28 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8704 (mppt) REVERT: U 16 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8482 (mm-30) REVERT: U 31 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8791 (mp) REVERT: U 41 TYR cc_start: 0.8870 (m-80) cc_final: 0.8565 (m-10) REVERT: V 50 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7412 (tp) REVERT: V 83 LYS cc_start: 0.7993 (mmpt) cc_final: 0.7560 (tptp) REVERT: W 94 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: W 108 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: Y 41 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7728 (mm-30) REVERT: Y 88 ASP cc_start: 0.8069 (t0) cc_final: 0.7857 (t70) REVERT: Y 94 ASP cc_start: 0.7846 (m-30) cc_final: 0.7427 (t0) REVERT: a 71 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8948 (ttm) REVERT: b 93 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8050 (mttp) REVERT: c 63 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8281 (pp20) REVERT: c 70 MET cc_start: 0.8879 (mmm) cc_final: 0.8618 (mmt) REVERT: d 32 TYR cc_start: 0.7637 (t80) cc_final: 0.7190 (m-80) REVERT: f 53 PHE cc_start: 0.8588 (t80) cc_final: 0.8192 (t80) REVERT: g 4 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8642 (mtt) REVERT: i 89 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8245 (tpt) REVERT: i 321 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7311 (mmmt) REVERT: k 97 GLN cc_start: 0.8621 (mp10) cc_final: 0.8351 (mp10) REVERT: l 207 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5634 (pp20) REVERT: l 484 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8553 (tp) REVERT: l 580 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6313 (mp10) REVERT: m 46 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8426 (t0) REVERT: m 98 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7411 (mmp) REVERT: n 48 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7448 (mp0) REVERT: o 31 LYS cc_start: 0.8467 (mtpm) cc_final: 0.7813 (mtmt) REVERT: o 118 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7101 (pt0) REVERT: r 378 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: r 453 MET cc_start: 0.8493 (mmp) cc_final: 0.8257 (mmt) REVERT: s 156 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8391 (mmt) REVERT: s 202 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: s 224 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: u 157 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7153 (m-30) REVERT: v 81 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7951 (mmpt) REVERT: v 103 GLU cc_start: 0.8459 (tp30) cc_final: 0.8177 (tp30) REVERT: w 261 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6669 (ttm110) REVERT: w 267 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7195 (tp30) outliers start: 89 outliers final: 35 residues processed: 721 average time/residue: 0.7842 time to fit residues: 674.7086 Evaluate side-chains 723 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 663 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 47 ASN Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 128 MET Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 207 GLU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 575 ILE Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 46 ASN Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 56 CYS Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 261 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 28 optimal weight: 8.9990 chunk 445 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 309 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 285 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 404 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN j 26 GLN k 83 ASN r 44 GLN r 304 GLN u 77 HIS v 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.094942 restraints weight = 51949.214| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.23 r_work: 0.2858 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40657 Z= 0.156 Angle : 0.574 9.727 54865 Z= 0.286 Chirality : 0.042 0.251 5930 Planarity : 0.004 0.048 6675 Dihedral : 15.239 177.000 6627 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 2.28 % Allowed : 13.51 % Favored : 84.21 % 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: 1.90 (0.12), residues: 4666 helix: 2.20 (0.09), residues: 2961 sheet: -1.25 (0.96), residues: 23 loop : -0.40 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG b 16 TYR 0.025 0.002 TYR l 587 PHE 0.028 0.002 PHE i 292 TRP 0.017 0.001 TRP u 86 HIS 0.008 0.001 HIS u 77 Details of bonding type rmsd covalent geometry : bond 0.00375 (40648) covalent geometry : angle 0.57270 (54849) SS BOND : bond 0.00318 ( 8) SS BOND : angle 1.98556 ( 16) hydrogen bonds : bond 0.04801 ( 2257) hydrogen bonds : angle 4.03240 ( 6594) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 667 time to evaluate : 1.609 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 52 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7699 (mmm) REVERT: U 16 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8501 (mm-30) REVERT: U 41 TYR cc_start: 0.8956 (m-80) cc_final: 0.8688 (m-10) REVERT: V 50 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7425 (tp) REVERT: V 83 LYS cc_start: 0.8071 (mmpt) cc_final: 0.7590 (tptp) REVERT: W 94 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: W 96 ILE cc_start: 0.8022 (mm) cc_final: 0.7788 (mt) REVERT: W 108 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: Y 88 ASP cc_start: 0.8069 (t0) cc_final: 0.7801 (t70) REVERT: Y 94 ASP cc_start: 0.7845 (m-30) cc_final: 0.7455 (t0) REVERT: a 69 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8433 (pttt) REVERT: a 71 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8967 (ttm) REVERT: b 93 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8085 (mttp) REVERT: d 32 TYR cc_start: 0.7771 (t80) cc_final: 0.7320 (m-80) REVERT: f 53 PHE cc_start: 0.8602 (t80) cc_final: 0.8116 (t80) REVERT: g 4 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8632 (mtp) REVERT: i 89 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8418 (tpt) REVERT: i 245 MET cc_start: 0.9094 (tmm) cc_final: 0.8753 (ttp) REVERT: i 321 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7381 (mmmt) REVERT: j 57 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8584 (tt) REVERT: k 97 GLN cc_start: 0.8640 (mp10) cc_final: 0.8389 (mp10) REVERT: l 163 ASP cc_start: 0.8576 (m-30) cc_final: 0.8315 (m-30) REVERT: l 207 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5640 (pp20) REVERT: l 484 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8559 (tp) REVERT: l 580 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6304 (mp10) REVERT: m 98 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7417 (mmp) REVERT: o 31 LYS cc_start: 0.8479 (mtpm) cc_final: 0.7819 (mtmt) REVERT: o 118 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7112 (pt0) REVERT: r 304 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8516 (mt0) REVERT: r 378 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: r 453 MET cc_start: 0.8555 (mmp) cc_final: 0.8310 (mmt) REVERT: s 156 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8437 (mmt) REVERT: s 224 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: u 157 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: v 81 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7977 (mmpt) REVERT: v 103 GLU cc_start: 0.8483 (tp30) cc_final: 0.8193 (tp30) REVERT: w 261 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6822 (ttm110) REVERT: w 267 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7221 (tp30) outliers start: 94 outliers final: 40 residues processed: 710 average time/residue: 0.8160 time to fit residues: 686.9566 Evaluate side-chains 715 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 652 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 47 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 207 GLU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 575 ILE Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 163 ILE Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 231 ILE Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 261 ARG Chi-restraints excluded: chain w residue 291 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 166 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 311 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 323 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 430 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN j 26 GLN k 83 ASN r 44 GLN r 304 GLN u 77 HIS v 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.096680 restraints weight = 51896.778| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.23 r_work: 0.2881 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.10 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) = 0.081 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40657 Z= 0.117 Angle : 0.542 11.559 54865 Z= 0.270 Chirality : 0.040 0.243 5930 Planarity : 0.004 0.046 6675 Dihedral : 14.883 167.206 6627 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.07 % Allowed : 14.09 % Favored : 83.84 % 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: 2.02 (0.12), residues: 4666 helix: 2.31 (0.09), residues: 2953 sheet: -1.20 (0.97), residues: 23 loop : -0.37 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 16 TYR 0.021 0.001 TYR l 587 PHE 0.026 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS u 77 Details of bonding type rmsd covalent geometry : bond 0.00263 (40648) covalent geometry : angle 0.54087 (54849) SS BOND : bond 0.00200 ( 8) SS BOND : angle 1.79597 ( 16) hydrogen bonds : bond 0.04331 ( 2257) hydrogen bonds : angle 3.96547 ( 6594) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 688 time to evaluate : 1.467 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: S 28 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8646 (mppt) REVERT: U 16 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8435 (mm-30) REVERT: U 41 TYR cc_start: 0.8955 (m-80) cc_final: 0.8636 (m-10) REVERT: V 50 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7407 (tp) REVERT: V 83 LYS cc_start: 0.7995 (mmpt) cc_final: 0.7538 (tptp) REVERT: W 94 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: W 96 ILE cc_start: 0.7994 (mm) cc_final: 0.7759 (mt) REVERT: W 108 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: Y 88 ASP cc_start: 0.8055 (t0) cc_final: 0.7843 (t70) REVERT: Y 94 ASP cc_start: 0.7830 (m-30) cc_final: 0.7544 (t0) REVERT: a 69 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8425 (pttt) REVERT: a 71 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8950 (ttm) REVERT: b 93 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8058 (mttp) REVERT: c 70 MET cc_start: 0.8890 (mmm) cc_final: 0.8645 (mmt) REVERT: d 32 TYR cc_start: 0.7725 (t80) cc_final: 0.7284 (m-80) REVERT: e 72 ASP cc_start: 0.8177 (p0) cc_final: 0.7805 (p0) REVERT: f 53 PHE cc_start: 0.8591 (t80) cc_final: 0.8113 (t80) REVERT: i 89 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8349 (tpt) REVERT: i 245 MET cc_start: 0.9103 (tmm) cc_final: 0.8787 (ttp) REVERT: i 321 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7303 (mmmt) REVERT: j 57 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8604 (tt) REVERT: k 97 GLN cc_start: 0.8624 (mp10) cc_final: 0.8391 (mp10) REVERT: l 207 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5549 (pp20) REVERT: l 484 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8573 (tp) REVERT: l 580 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.6308 (mp10) REVERT: m 98 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7416 (mmp) REVERT: m 135 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: n 48 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7457 (mp0) REVERT: o 31 LYS cc_start: 0.8484 (mtpm) cc_final: 0.7844 (mtmt) REVERT: o 118 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7109 (pt0) REVERT: p 179 MET cc_start: 0.7503 (mtt) cc_final: 0.6771 (mtt) REVERT: r 378 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: r 453 MET cc_start: 0.8546 (mmp) cc_final: 0.8310 (mmt) REVERT: s 156 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8252 (mmt) REVERT: s 224 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: u 157 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: v 15 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8299 (mtpp) REVERT: v 81 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7993 (mmpt) REVERT: v 103 GLU cc_start: 0.8467 (tp30) cc_final: 0.8179 (tp30) REVERT: w 261 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6837 (ttm110) REVERT: w 267 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7187 (tp30) outliers start: 85 outliers final: 41 residues processed: 729 average time/residue: 0.8068 time to fit residues: 704.5182 Evaluate side-chains 728 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 665 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 47 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 207 GLU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 575 ILE Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 261 ARG Chi-restraints excluded: chain w residue 291 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 93 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 441 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 315 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN j 26 GLN k 83 ASN p 62 GLN r 44 GLN r 304 GLN u 64 ASN u 77 HIS v 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.093550 restraints weight = 52170.197| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.23 r_work: 0.2831 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 40657 Z= 0.188 Angle : 0.612 11.569 54865 Z= 0.305 Chirality : 0.044 0.267 5930 Planarity : 0.005 0.048 6675 Dihedral : 15.086 169.484 6627 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 2.07 % Allowed : 14.33 % Favored : 83.60 % 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: 1.76 (0.12), residues: 4666 helix: 2.09 (0.09), residues: 2961 sheet: -1.37 (0.93), residues: 23 loop : -0.45 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 16 TYR 0.027 0.002 TYR l 587 PHE 0.028 0.002 PHE i 292 TRP 0.015 0.001 TRP u 86 HIS 0.013 0.001 HIS u 77 Details of bonding type rmsd covalent geometry : bond 0.00458 (40648) covalent geometry : angle 0.61119 (54849) SS BOND : bond 0.00363 ( 8) SS BOND : angle 2.19580 ( 16) hydrogen bonds : bond 0.05229 ( 2257) hydrogen bonds : angle 4.10847 ( 6594) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 658 time to evaluate : 1.557 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 16 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: U 41 TYR cc_start: 0.8996 (m-80) cc_final: 0.8691 (m-10) REVERT: W 94 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: W 108 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: Y 88 ASP cc_start: 0.8078 (t0) cc_final: 0.7812 (t70) REVERT: Y 94 ASP cc_start: 0.8031 (m-30) cc_final: 0.7631 (t0) REVERT: a 69 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8452 (pttt) REVERT: a 71 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8967 (ttm) REVERT: b 16 ARG cc_start: 0.8268 (mtm110) cc_final: 0.8039 (ptp-110) REVERT: b 93 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8185 (mttp) REVERT: d 32 TYR cc_start: 0.7812 (t80) cc_final: 0.7330 (m-80) REVERT: f 53 PHE cc_start: 0.8600 (t80) cc_final: 0.8108 (t80) REVERT: i 89 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8435 (tpt) REVERT: i 245 MET cc_start: 0.9102 (tmm) cc_final: 0.8768 (ttp) REVERT: i 321 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7444 (mmmt) REVERT: j 57 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8600 (tt) REVERT: k 97 GLN cc_start: 0.8648 (mp10) cc_final: 0.8378 (mp10) REVERT: l 163 ASP cc_start: 0.8601 (m-30) cc_final: 0.8338 (m-30) REVERT: l 207 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.5655 (pp20) REVERT: l 484 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8605 (tp) REVERT: l 580 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6308 (mp10) REVERT: m 60 TYR cc_start: 0.9166 (m-80) cc_final: 0.8866 (m-80) REVERT: m 98 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7354 (mmp) REVERT: o 31 LYS cc_start: 0.8550 (mtpm) cc_final: 0.7865 (mtmt) REVERT: o 118 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7135 (pt0) REVERT: r 378 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: r 453 MET cc_start: 0.8521 (mmp) cc_final: 0.8270 (mmt) REVERT: s 156 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8226 (mmt) REVERT: u 157 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: v 81 LYS cc_start: 0.8370 (mtpp) cc_final: 0.8106 (mmpt) REVERT: v 103 GLU cc_start: 0.8501 (tp30) cc_final: 0.8267 (tp30) REVERT: w 261 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6642 (ttm110) REVERT: w 267 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7211 (tp30) outliers start: 85 outliers final: 42 residues processed: 701 average time/residue: 0.8003 time to fit residues: 667.7930 Evaluate side-chains 707 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 647 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 47 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 207 GLU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 575 ILE Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 261 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 369 optimal weight: 0.0570 chunk 140 optimal weight: 5.9990 chunk 392 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 20 optimal weight: 0.0570 chunk 178 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 415 optimal weight: 0.0770 chunk 227 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN j 26 GLN l 405 ASN r 44 GLN r 304 GLN u 77 HIS v 50 GLN v 76 ASN v 85 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098430 restraints weight = 51845.132| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.23 r_work: 0.2908 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 40657 Z= 0.106 Angle : 0.534 12.234 54865 Z= 0.266 Chirality : 0.039 0.231 5930 Planarity : 0.004 0.045 6675 Dihedral : 14.354 172.169 6627 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.58 % Allowed : 14.92 % Favored : 83.50 % 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: 2.07 (0.13), residues: 4666 helix: 2.33 (0.09), residues: 2962 sheet: -1.15 (0.96), residues: 23 loop : -0.33 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG b 16 TYR 0.021 0.001 TYR l 422 PHE 0.028 0.001 PHE i 292 TRP 0.023 0.001 TRP l 144 HIS 0.007 0.001 HIS u 77 Details of bonding type rmsd covalent geometry : bond 0.00223 (40648) covalent geometry : angle 0.53345 (54849) SS BOND : bond 0.00194 ( 8) SS BOND : angle 1.62107 ( 16) hydrogen bonds : bond 0.03996 ( 2257) hydrogen bonds : angle 3.93658 ( 6594) Misc. bond : bond 0.00011 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 693 time to evaluate : 1.562 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 52 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7692 (mmm) REVERT: S 28 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8665 (mppt) REVERT: U 41 TYR cc_start: 0.8973 (m-80) cc_final: 0.8662 (m-10) REVERT: V 50 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7388 (tp) REVERT: V 83 LYS cc_start: 0.7986 (mmpt) cc_final: 0.7527 (tptp) REVERT: W 108 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: Y 88 ASP cc_start: 0.8062 (t0) cc_final: 0.7805 (t70) REVERT: Y 94 ASP cc_start: 0.7842 (m-30) cc_final: 0.7527 (t0) REVERT: a 69 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8396 (pttt) REVERT: a 71 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8910 (ttm) REVERT: b 16 ARG cc_start: 0.8217 (mtm110) cc_final: 0.7976 (ptp-110) REVERT: c 63 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8173 (pp20) REVERT: c 70 MET cc_start: 0.8910 (mmm) cc_final: 0.8682 (mmt) REVERT: d 32 TYR cc_start: 0.7660 (t80) cc_final: 0.7263 (m-80) REVERT: e 72 ASP cc_start: 0.8171 (p0) cc_final: 0.7839 (p0) REVERT: f 53 PHE cc_start: 0.8579 (t80) cc_final: 0.8085 (t80) REVERT: g 109 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8198 (mtmp) REVERT: i 68 MET cc_start: 0.9224 (mmt) cc_final: 0.9002 (mmp) REVERT: i 89 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8213 (tpt) REVERT: i 321 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7314 (mmmt) REVERT: j 57 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8602 (tt) REVERT: k 97 GLN cc_start: 0.8620 (mp10) cc_final: 0.8236 (mp10) REVERT: l 484 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8567 (tp) REVERT: l 580 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6292 (mp10) REVERT: m 60 TYR cc_start: 0.9046 (m-80) cc_final: 0.8690 (m-80) REVERT: m 98 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7346 (mmp) REVERT: n 48 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7491 (mp0) REVERT: o 31 LYS cc_start: 0.8500 (mtpm) cc_final: 0.7882 (mtmt) REVERT: o 118 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7128 (pt0) REVERT: r 123 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8327 (tp30) REVERT: r 378 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: r 453 MET cc_start: 0.8490 (mmp) cc_final: 0.8217 (mmt) REVERT: u 157 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: v 15 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8271 (mtpp) REVERT: v 81 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7918 (mmpt) REVERT: v 103 GLU cc_start: 0.8435 (tp30) cc_final: 0.8195 (tp30) REVERT: w 267 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7165 (tp30) outliers start: 65 outliers final: 35 residues processed: 722 average time/residue: 0.7860 time to fit residues: 677.0271 Evaluate side-chains 729 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 679 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 47 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 575 ILE Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain w residue 53 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 322 optimal weight: 4.9990 chunk 7 optimal weight: 0.0010 chunk 228 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 382 optimal weight: 3.9990 chunk 412 optimal weight: 3.9990 chunk 130 optimal weight: 50.0000 chunk 98 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN j 26 GLN k 83 ASN r 44 GLN r 51 ASN r 304 GLN u 77 HIS v 50 GLN v 76 ASN v 85 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.095124 restraints weight = 52210.329| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.24 r_work: 0.2865 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 40657 Z= 0.149 Angle : 0.579 12.107 54865 Z= 0.288 Chirality : 0.042 0.234 5930 Planarity : 0.004 0.048 6675 Dihedral : 14.369 175.922 6627 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.48 % Allowed : 15.45 % Favored : 83.07 % 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: 1.95 (0.12), residues: 4666 helix: 2.22 (0.09), residues: 2968 sheet: -1.12 (0.96), residues: 23 loop : -0.36 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 16 TYR 0.024 0.001 TYR l 587 PHE 0.028 0.002 PHE i 292 TRP 0.017 0.001 TRP u 86 HIS 0.009 0.001 HIS u 77 Details of bonding type rmsd covalent geometry : bond 0.00356 (40648) covalent geometry : angle 0.57806 (54849) SS BOND : bond 0.00304 ( 8) SS BOND : angle 1.87461 ( 16) hydrogen bonds : bond 0.04670 ( 2257) hydrogen bonds : angle 4.00860 ( 6594) Misc. bond : bond 0.00040 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16089.25 seconds wall clock time: 273 minutes 40.88 seconds (16420.88 seconds total)