Starting phenix.real_space_refine on Sat Mar 7 07:57:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vxs_32187/03_2026/7vxs_32187.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vxs_32187/03_2026/7vxs_32187.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/7vxs_32187/03_2026/7vxs_32187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vxs_32187/03_2026/7vxs_32187.map" model { file = "/net/cci-nas-00/data/ceres_data/7vxs_32187/03_2026/7vxs_32187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vxs_32187/03_2026/7vxs_32187.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= 0.004 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 37 5.49 5 S 293 5.16 5 C 26074 2.51 5 N 6284 2.21 5 O 6986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 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: 39674 Number of models: 1 Model: "" Number of chains: 43 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: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 694 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 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: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1291 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 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: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2590 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} 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: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 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: "i" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 115 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "j" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "l" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 290 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "r" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 203 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 181 Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 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=0.67 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.67 Time building chain proxies: 7.12, per 1000 atoms: 0.18 Number of scatterers: 39674 At special positions: 0 Unit cell: (183.688, 190.133, 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 37 15.00 O 6986 8.00 N 6284 7.00 C 26074 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=1.60 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.4 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: 217 helices and 6 sheets defined 69.6% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 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 56 through 61 removed outlier: 4.121A 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: 3.610A pdb=" N ILE S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 41 through 56 removed outlier: 4.211A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'U' and resid 3 through 16 removed outlier: 3.716A pdb=" N SER U 7 " --> pdb=" O GLY U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 36 removed outlier: 3.586A pdb=" N VAL U 20 " --> pdb=" O GLU U 16 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 78 through 83 removed outlier: 3.592A pdb=" N ASN U 83 " --> pdb=" O GLU U 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 12 removed outlier: 3.924A 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: 4.144A 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 138 Processing helix chain 'W' and resid 138 through 143 Processing helix chain 'X' and resid 75 through 89 Processing helix chain 'X' and resid 111 through 127 Processing helix chain 'X' and resid 140 through 153 Processing helix chain 'Y' and resid 51 through 76 Processing helix chain 'Y' and resid 77 through 82 Processing helix chain 'Y' and resid 88 through 92 Processing helix chain 'Z' and resid 18 through 22 removed outlier: 3.572A pdb=" N GLN Z 21 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 3.888A 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: 3.742A pdb=" N THR Z 31 " --> pdb=" O THR Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 47 removed outlier: 3.856A pdb=" N GLY Z 46 " --> pdb=" O ASP Z 43 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG Z 47 " --> pdb=" O PRO Z 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 43 through 47' Processing helix chain 'Z' and resid 50 through 55 removed outlier: 3.805A pdb=" N GLY Z 55 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 68 Processing helix chain 'Z' and resid 70 through 87 removed outlier: 3.507A pdb=" N TYR Z 87 " --> pdb=" O GLY Z 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 93 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 108 through 113 removed outlier: 4.140A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) removed outlier: 4.086A 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: 4.013A pdb=" N ASN a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 removed outlier: 3.557A pdb=" N LEU a 178 " --> pdb=" O ASP a 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 26 Processing helix chain 'b' and resid 68 through 75 removed outlier: 3.975A pdb=" N VAL b 72 " --> pdb=" O SER b 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'c' and resid 33 through 37 removed outlier: 3.739A 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 149 Processing helix chain 'd' and resid 28 through 58 removed outlier: 3.748A pdb=" N TYR d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 81 through 117 Processing helix chain 'd' and resid 120 through 125 removed outlier: 4.040A pdb=" N CYS d 125 " --> pdb=" O TYR d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 144 removed outlier: 3.813A 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 79 through 95 Processing helix chain 'e' and resid 97 through 108 removed outlier: 3.565A pdb=" N TYR e 108 " --> pdb=" O THR e 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 through 133 Processing helix chain 'e' and resid 143 through 147 Processing helix chain 'f' and resid 40 through 74 Processing helix chain 'g' and resid 17 through 23 Processing helix chain 'g' and resid 30 through 51 Processing helix chain 'g' and resid 59 through 99 removed outlier: 3.791A 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 removed outlier: 3.663A pdb=" N ARG h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 45 Processing helix chain 'h' and resid 48 through 53 removed outlier: 3.637A pdb=" N GLU h 53 " --> pdb=" O GLY h 49 " (cutoff:3.500A) Processing helix chain 'h' and resid 56 through 69 Processing helix chain 'h' and resid 69 through 90 Processing helix chain 'h' and resid 95 through 99 Processing helix chain 'i' and resid 2 through 23 Processing helix chain 'i' and resid 25 through 45 Proline residue: i 42 - end of helix removed outlier: 3.724A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 81 Processing helix chain 'i' and resid 91 through 107 Processing helix chain 'i' and resid 113 through 122 removed outlier: 4.253A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 133 Processing helix chain 'i' and resid 135 through 145 Processing helix chain 'i' and resid 146 through 149 Processing helix chain 'i' and resid 150 through 170 removed outlier: 3.660A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 174 through 193 removed outlier: 3.873A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 197 through 222 removed outlier: 3.714A 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 253 removed outlier: 3.528A pdb=" N GLY i 253 " --> pdb=" O LEU i 249 " (cutoff:3.500A) Processing helix chain 'i' and resid 259 through 272 removed outlier: 4.421A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 3.549A pdb=" N THR i 280 " --> pdb=" O ILE i 276 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 3.755A pdb=" N LYS i 314 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 325 through 335 Processing helix chain 'i' and resid 336 through 347 Proline residue: i 341 - end of helix removed outlier: 3.502A pdb=" N ASN i 347 " --> pdb=" O SER i 344 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 55 through 73 removed outlier: 4.135A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 79 Processing helix chain 'j' and resid 83 through 108 removed outlier: 3.541A pdb=" N MET j 87 " --> pdb=" O ASN j 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 22 removed outlier: 3.583A pdb=" N MET k 6 " --> pdb=" O PRO k 2 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR k 22 " --> pdb=" O GLY k 18 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 57 through 86 removed outlier: 4.658A pdb=" N ILE k 61 " --> pdb=" O ASN k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 89 through 93 removed outlier: 3.558A pdb=" N ASN k 92 " --> pdb=" O TYR k 89 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 14 removed outlier: 4.401A pdb=" N SER l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 21 Processing helix chain 'l' and resid 22 through 24 No H-bonds generated for 'chain 'l' and resid 22 through 24' Processing helix chain 'l' and resid 31 through 58 removed outlier: 4.467A 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: 3.894A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 133 Processing helix chain 'l' and resid 136 through 156 Processing helix chain 'l' and resid 161 through 194 removed outlier: 3.883A 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: 4.188A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.752A 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 Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 4.064A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.886A 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 382 Processing helix chain 'l' and resid 388 through 401 removed outlier: 4.824A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 405 through 432 removed outlier: 3.742A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 470 removed outlier: 5.767A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 483 through 488 Processing helix chain 'l' and resid 488 through 507 Processing helix chain 'l' and resid 508 through 510 No H-bonds generated for 'chain 'l' and resid 508 through 510' Processing helix chain 'l' and resid 517 through 525 Processing helix chain 'l' and resid 528 through 534 Processing helix chain 'l' and resid 535 through 548 Processing helix chain 'l' and resid 556 through 562 removed outlier: 3.806A pdb=" N LEU l 562 " --> pdb=" O LEU l 558 " (cutoff:3.500A) Processing helix chain 'l' and resid 562 through 578 Processing helix chain 'l' and resid 583 through 602 removed outlier: 3.926A pdb=" N TYR l 587 " --> pdb=" O LEU l 583 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 22 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 49 through 75 Processing helix chain 'm' and resid 86 through 110 Processing helix chain 'm' and resid 137 through 145 Processing helix chain 'm' and resid 150 through 172 Processing helix chain 'n' and resid 4 through 12 Processing helix chain 'n' and resid 15 through 33 Processing helix chain 'o' and resid 15 through 18 Processing helix chain 'o' and resid 19 through 24 removed outlier: 4.253A pdb=" N TYR o 23 " --> pdb=" O ASP o 19 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 52 removed outlier: 3.712A 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 119 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 11 through 31 Processing helix chain 'p' and resid 33 through 51 removed outlier: 4.316A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 74 Processing helix chain 'p' and resid 92 through 97 removed outlier: 3.538A pdb=" N GLU p 95 " --> pdb=" O GLU p 92 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 100 through 107 Processing helix chain 'p' and resid 108 through 114 removed outlier: 3.899A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 143 removed outlier: 3.544A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'r' and resid 2 through 17 Proline residue: r 7 - end of helix 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: 3.968A 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: 4.146A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 88 through 111 removed outlier: 3.608A 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 136 removed outlier: 3.852A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 171 removed outlier: 4.080A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.665A 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 207 removed outlier: 4.493A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 4.256A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 224 through 234 Processing helix chain 'r' and resid 236 through 251 removed outlier: 4.157A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU r 250 " --> pdb=" O ILE r 246 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN r 251 " --> pdb=" O THR r 247 " (cutoff:3.500A) Processing helix chain 'r' and resid 252 through 258 removed outlier: 4.328A pdb=" N TYR r 256 " --> pdb=" O PRO r 252 " (cutoff:3.500A) Processing helix chain 'r' and resid 258 through 278 removed outlier: 3.816A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 304 removed outlier: 3.637A pdb=" N ILE r 286 " --> pdb=" O LEU r 282 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN r 304 " --> pdb=" O ALA r 300 " (cutoff:3.500A) Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.523A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (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: 4.178A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN r 415 " --> pdb=" O LEU r 411 " (cutoff:3.500A) Processing helix chain 'r' and resid 430 through 450 removed outlier: 3.544A pdb=" N ASN r 434 " --> pdb=" O PHE r 430 " (cutoff:3.500A) Proline residue: r 443 - end of helix removed outlier: 3.565A pdb=" N ASN r 450 " --> pdb=" O LEU r 446 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 455 removed outlier: 3.775A 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: 3.727A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 Processing helix chain 's' and resid 46 through 57 Processing helix chain 's' and resid 67 through 85 Proline residue: s 75 - end of helix Processing helix chain 's' and resid 100 through 124 removed outlier: 3.566A pdb=" N PHE s 104 " --> pdb=" O LEU s 100 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN s 124 " --> pdb=" O GLY s 120 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 5.107A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 3.891A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN s 169 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 177 Processing helix chain 's' and resid 178 through 193 Processing helix chain 's' and resid 203 through 208 removed outlier: 3.540A pdb=" N VAL s 208 " --> pdb=" O GLU s 204 " (cutoff:3.500A) Processing helix chain 's' and resid 209 through 214 removed outlier: 3.596A pdb=" N ASN s 212 " --> pdb=" O SER s 209 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU s 214 " --> pdb=" O PHE s 211 " (cutoff:3.500A) Processing helix chain 's' and resid 217 through 243 removed outlier: 3.623A pdb=" N ALA s 221 " --> pdb=" O ALA s 217 " (cutoff:3.500A) Processing helix chain 's' and resid 252 through 277 Processing helix chain 's' and resid 281 through 292 removed outlier: 3.972A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 292 through 312 removed outlier: 4.107A 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 9 through 14 removed outlier: 3.710A pdb=" N LYS u 14 " --> pdb=" O GLU u 11 " (cutoff:3.500A) Processing helix chain 'u' and resid 21 through 28 Processing helix chain 'u' and resid 28 through 36 Processing helix chain 'u' and resid 36 through 51 removed outlier: 3.568A pdb=" N ASN u 40 " --> pdb=" O CYS u 36 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 55 Processing helix chain 'u' and resid 56 through 78 removed outlier: 3.596A pdb=" N GLY u 60 " --> pdb=" O CYS u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 78 through 92 removed outlier: 3.895A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 115 Processing helix chain 'v' and resid 3 through 11 Processing helix chain 'v' and resid 42 through 50 Processing helix chain 'v' and resid 59 through 73 removed outlier: 3.742A pdb=" N LEU v 63 " --> pdb=" O CYS v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 125 removed outlier: 4.137A pdb=" N GLY v 125 " --> pdb=" O GLU v 121 " (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 97 Processing helix chain 'w' and resid 113 through 120 Processing helix chain 'w' and resid 126 through 154 Processing helix chain 'w' and resid 162 through 165 Processing helix chain 'w' and resid 166 through 176 removed outlier: 3.957A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 195 removed outlier: 3.830A pdb=" N VAL w 184 " --> pdb=" O ARG w 180 " (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: 3.815A 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 250 removed outlier: 3.596A pdb=" N LEU w 234 " --> pdb=" O THR w 230 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix Processing helix chain 'w' and resid 260 through 264 removed outlier: 3.518A pdb=" N ALA w 263 " --> pdb=" O ALA w 260 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU w 264 " --> pdb=" O ARG w 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 260 through 264' Processing helix chain 'w' and resid 265 through 275 removed outlier: 3.703A pdb=" N VAL w 269 " --> pdb=" O ASP w 265 " (cutoff:3.500A) Processing helix chain 'w' and resid 282 through 286 Processing helix chain 'w' and resid 287 through 299 Processing helix chain 'w' and resid 300 through 306 removed outlier: 3.711A pdb=" N VAL w 304 " --> pdb=" O ASN w 300 " (cutoff:3.500A) Processing helix chain 'w' and resid 307 through 309 No H-bonds generated for 'chain 'w' and resid 307 through 309' 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: 6.305A 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: 5.507A 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: 5.288A pdb=" N SER l 64 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE l 80 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP l 66 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU l 76 " --> pdb=" O TRP l 68 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR l 70 " --> pdb=" O VAL l 74 " (cutoff:3.500A) removed outlier: 6.560A 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 'r' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'w' and resid 84 through 86 removed outlier: 6.429A pdb=" N ILE w 60 " --> pdb=" O LEU w 159 " (cutoff:3.500A) 2294 hydrogen bonds defined for protein. 6684 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: 6.41 Time building geometry restraints manager: 4.75 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: 5984 1.31 - 1.44: 10976 1.44 - 1.57: 23023 1.57 - 1.70: 171 1.70 - 1.82: 529 Bond restraints: 40683 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 1.27e+02 bond pdb=" CB7 CDL i 401 " pdb=" OB8 CDL i 401 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDL i 401 " pdb=" OA8 CDL i 401 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDL n 102 " pdb=" OA8 CDL n 102 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CA7 CDL l 702 " pdb=" OA8 CDL l 702 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 ... (remaining 40678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 54247 3.46 - 6.92: 511 6.92 - 10.38: 99 10.38 - 13.84: 15 13.84 - 17.30: 9 Bond angle restraints: 54881 Sorted by residual: angle pdb=" C ASP Z 43 " pdb=" N PRO Z 44 " pdb=" CA PRO Z 44 " ideal model delta sigma weight residual 118.85 131.71 -12.86 1.09e+00 8.42e-01 1.39e+02 angle pdb=" N ILE s 68 " pdb=" CA ILE s 68 " pdb=" C ILE s 68 " ideal model delta sigma weight residual 110.62 118.58 -7.96 1.02e+00 9.61e-01 6.08e+01 angle pdb=" C ARG s 62 " pdb=" N PRO s 63 " pdb=" CA PRO s 63 " ideal model delta sigma weight residual 119.78 127.72 -7.94 1.03e+00 9.43e-01 5.94e+01 angle pdb=" C11 CDL l 702 " pdb=" CA5 CDL l 702 " pdb=" OA6 CDL l 702 " ideal model delta sigma weight residual 111.33 121.25 -9.92 1.32e+00 5.72e-01 5.64e+01 angle pdb=" N MET b 120 " pdb=" CA MET b 120 " pdb=" C MET b 120 " ideal model delta sigma weight residual 109.39 121.19 -11.80 1.59e+00 3.96e-01 5.50e+01 ... (remaining 54876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 23494 35.12 - 70.24: 1270 70.24 - 105.36: 74 105.36 - 140.48: 25 140.48 - 175.60: 19 Dihedral angle restraints: 24882 sinusoidal: 11022 harmonic: 13860 Sorted by residual: dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 96.24 -156.24 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" CA ARG c 114 " pdb=" C ARG c 114 " pdb=" N ASN c 115 " pdb=" CA ASN c 115 " ideal model delta harmonic sigma weight residual 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA SER m 25 " pdb=" C SER m 25 " pdb=" N PRO m 26 " pdb=" CA PRO m 26 " ideal model delta harmonic sigma weight residual 180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 24879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5523 0.079 - 0.158: 377 0.158 - 0.238: 22 0.238 - 0.317: 4 0.317 - 0.396: 5 Chirality restraints: 5931 Sorted by residual: chirality pdb=" CA MET b 120 " pdb=" N MET b 120 " pdb=" C MET b 120 " pdb=" CB MET b 120 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA LYS b 121 " pdb=" N LYS b 121 " pdb=" C LYS b 121 " pdb=" CB LYS b 121 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA THR a 185 " pdb=" N THR a 185 " pdb=" C THR a 185 " pdb=" CB THR a 185 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 5928 not shown) Planarity restraints: 6676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG n 50 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO n 51 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO n 51 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO n 51 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET r 401 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C MET r 401 " 0.035 2.00e-02 2.50e+03 pdb=" O MET r 401 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE r 402 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER r 407 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C SER r 407 " 0.035 2.00e-02 2.50e+03 pdb=" O SER r 407 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU r 408 " -0.012 2.00e-02 2.50e+03 ... (remaining 6673 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 432 2.64 - 3.20: 35118 3.20 - 3.77: 61842 3.77 - 4.33: 85840 4.33 - 4.90: 144311 Nonbonded interactions: 327543 Sorted by model distance: nonbonded pdb=" OE2 GLU Z 49 " pdb=" NE ARG p 34 " model vdw 2.074 3.120 nonbonded pdb=" OH TYR o 23 " pdb=" OE1 GLU p 68 " model vdw 2.103 3.040 nonbonded pdb=" OE2 GLU Z 49 " pdb=" NH2 ARG p 34 " model vdw 2.117 3.120 nonbonded pdb=" OD1 ASP a 188 " pdb=" NH2 ARG u 47 " model vdw 2.117 3.120 nonbonded pdb=" O ASP Y 76 " pdb=" OH TYR l 385 " model vdw 2.151 3.040 ... (remaining 327538 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=0.67 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 29.780 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.903 40693 Z= 0.628 Angle : 0.865 34.420 54897 Z= 0.439 Chirality : 0.043 0.396 5931 Planarity : 0.004 0.075 6676 Dihedral : 20.068 175.597 15904 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 1.04 % Allowed : 15.39 % Favored : 83.57 % Cbeta Deviations : 0.02 % 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: 1.66 (0.13), residues: 4666 helix: 2.18 (0.10), residues: 2917 sheet: -0.41 (0.87), residues: 40 loop : -0.80 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG w 72 TYR 0.019 0.001 TYR l 422 PHE 0.030 0.001 PHE i 292 TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00726 (40683) covalent geometry : angle 0.85174 (54881) SS BOND : bond 0.15220 ( 8) SS BOND : angle 8.94169 ( 16) hydrogen bonds : bond 0.12514 ( 2294) hydrogen bonds : angle 5.15652 ( 6684) Misc. bond : bond 0.65255 ( 2) *********************** 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 720 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 677 time to evaluate : 1.517 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: a 58 LYS cc_start: 0.9019 (mtmp) cc_final: 0.8663 (mtpp) REVERT: g 27 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8207 (mttm) REVERT: o 111 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8279 (mtmt) REVERT: w 51 ARG cc_start: 0.8396 (ptp-170) cc_final: 0.8135 (mtm-85) REVERT: w 227 MET cc_start: 0.8524 (mpp) cc_final: 0.8169 (mpp) outliers start: 43 outliers final: 25 residues processed: 708 average time/residue: 0.7914 time to fit residues: 668.3483 Evaluate side-chains 688 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 663 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 79 SER Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 343 SER Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN ** a 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN g 18 ASN h 21 GLN h 27 HIS i 172 GLN i 319 HIS k 57 ASN l 109 HIS l 135 ASN l 199 GLN l 580 GLN n 3 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.078554 restraints weight = 57577.592| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.80 r_work: 0.2743 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40693 Z= 0.153 Angle : 0.563 10.023 54897 Z= 0.283 Chirality : 0.041 0.218 5931 Planarity : 0.004 0.057 6676 Dihedral : 19.110 173.707 6696 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 2.40 % Allowed : 13.64 % Favored : 83.96 % 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: 1.82 (0.13), residues: 4666 helix: 2.26 (0.09), residues: 2951 sheet: -1.00 (0.79), residues: 40 loop : -0.69 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 59 TYR 0.023 0.001 TYR l 587 PHE 0.031 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00358 (40683) covalent geometry : angle 0.56222 (54881) SS BOND : bond 0.00664 ( 8) SS BOND : angle 1.53599 ( 16) hydrogen bonds : bond 0.05134 ( 2294) hydrogen bonds : angle 4.18846 ( 6684) Misc. bond : bond 0.00724 ( 2) *********************** 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 775 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 676 time to evaluate : 1.409 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: W 98 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7227 (mpt) REVERT: X 98 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8350 (pt) REVERT: Y 62 SER cc_start: 0.8764 (m) cc_final: 0.8558 (m) REVERT: Z 25 GLU cc_start: 0.8086 (pm20) cc_final: 0.7689 (pm20) REVERT: a 189 ASN cc_start: 0.6982 (m-40) cc_final: 0.6715 (m-40) REVERT: b 99 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: c 34 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8132 (mmmt) REVERT: d 73 ASP cc_start: 0.8521 (p0) cc_final: 0.8236 (p0) REVERT: e 146 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8046 (mttp) REVERT: g 27 LYS cc_start: 0.8653 (mtmm) cc_final: 0.8248 (mttm) REVERT: g 113 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8328 (pt0) REVERT: h 65 GLU cc_start: 0.9113 (tp30) cc_final: 0.8807 (tm-30) REVERT: l 111 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8668 (t70) REVERT: l 596 MET cc_start: 0.8684 (mtp) cc_final: 0.8482 (mtp) REVERT: n 30 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7575 (mtp180) REVERT: o 111 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8267 (mtmt) REVERT: s 62 ARG cc_start: 0.8356 (ptt90) cc_final: 0.7734 (ptt-90) REVERT: w 75 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7569 (mtp85) REVERT: w 227 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7794 (mpt) REVERT: w 287 ASP cc_start: 0.7266 (t0) cc_final: 0.6912 (t0) outliers start: 99 outliers final: 39 residues processed: 716 average time/residue: 0.7786 time to fit residues: 667.7570 Evaluate side-chains 690 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 644 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 11 ASN Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 233 MET Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 227 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 343 optimal weight: 0.5980 chunk 216 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 274 optimal weight: 0.5980 chunk 335 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 327 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 62 ASN ** a 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN d 149 HIS e 148 GLN g 18 ASN i 319 HIS l 109 HIS l 135 ASN l 199 GLN n 3 ASN p 66 GLN r 139 GLN r 399 ASN v 47 ASN w 132 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.078731 restraints weight = 57407.035| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.77 r_work: 0.2751 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 40693 Z= 0.132 Angle : 0.535 8.516 54897 Z= 0.270 Chirality : 0.040 0.214 5931 Planarity : 0.004 0.057 6676 Dihedral : 17.821 173.528 6673 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 2.67 % Allowed : 14.68 % Favored : 82.65 % 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 (0.13), residues: 4666 helix: 2.32 (0.09), residues: 2953 sheet: -1.20 (0.78), residues: 40 loop : -0.65 (0.16), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG w 72 TYR 0.022 0.001 TYR l 587 PHE 0.029 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00304 (40683) covalent geometry : angle 0.53476 (54881) SS BOND : bond 0.00284 ( 8) SS BOND : angle 1.34239 ( 16) hydrogen bonds : bond 0.04735 ( 2294) hydrogen bonds : angle 4.01631 ( 6684) Misc. bond : bond 0.00473 ( 2) *********************** 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 795 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 685 time to evaluate : 1.517 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: S 4 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8676 (mt-10) REVERT: W 98 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7247 (mpt) REVERT: X 98 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8331 (pt) REVERT: Y 62 SER cc_start: 0.8727 (m) cc_final: 0.8518 (m) REVERT: Z 14 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.5613 (pp-130) REVERT: Z 85 GLU cc_start: 0.5337 (tt0) cc_final: 0.4964 (tt0) REVERT: a 189 ASN cc_start: 0.6913 (m-40) cc_final: 0.6653 (m-40) REVERT: b 99 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: c 34 LYS cc_start: 0.8528 (mmmt) cc_final: 0.8143 (mmmt) REVERT: d 73 ASP cc_start: 0.8503 (p0) cc_final: 0.8300 (p0) REVERT: g 27 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8243 (mttm) REVERT: g 113 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8434 (pt0) REVERT: h 13 ASP cc_start: 0.9198 (t0) cc_final: 0.8886 (t0) REVERT: h 65 GLU cc_start: 0.9128 (tp30) cc_final: 0.8845 (tm-30) REVERT: l 111 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8645 (t70) REVERT: m 139 GLU cc_start: 0.8570 (tt0) cc_final: 0.8285 (tt0) REVERT: n 30 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7576 (mtp180) REVERT: o 111 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8263 (mtmt) REVERT: v 53 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8642 (tp) REVERT: w 51 ARG cc_start: 0.8537 (ptp-170) cc_final: 0.8249 (mtm-85) REVERT: w 75 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7519 (mtp85) REVERT: w 120 ASP cc_start: 0.8443 (t70) cc_final: 0.8120 (t70) REVERT: w 227 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8303 (mpp) REVERT: w 287 ASP cc_start: 0.7323 (t0) cc_final: 0.6936 (t0) outliers start: 110 outliers final: 47 residues processed: 731 average time/residue: 0.7558 time to fit residues: 664.7862 Evaluate side-chains 702 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 646 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 385 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 237 optimal weight: 0.0570 chunk 438 optimal weight: 5.9990 chunk 404 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 62 ASN ** a 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN g 18 ASN i 319 HIS l 109 HIS n 3 ASN p 66 GLN v 47 ASN w 239 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.076205 restraints weight = 57656.135| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.78 r_work: 0.2711 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 40693 Z= 0.184 Angle : 0.575 10.858 54897 Z= 0.290 Chirality : 0.043 0.238 5931 Planarity : 0.004 0.065 6676 Dihedral : 17.242 169.359 6671 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.16 % Rotamer: Outliers : 2.74 % Allowed : 15.39 % Favored : 81.87 % 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: 1.80 (0.13), residues: 4666 helix: 2.24 (0.09), residues: 2960 sheet: -1.51 (0.81), residues: 35 loop : -0.69 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG w 72 TYR 0.026 0.001 TYR l 587 PHE 0.033 0.002 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS v 61 Details of bonding type rmsd covalent geometry : bond 0.00450 (40683) covalent geometry : angle 0.57447 (54881) SS BOND : bond 0.00371 ( 8) SS BOND : angle 1.47395 ( 16) hydrogen bonds : bond 0.05270 ( 2294) hydrogen bonds : angle 4.05796 ( 6684) Misc. bond : bond 0.00097 ( 2) *********************** 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 778 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 665 time to evaluate : 1.442 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: S 4 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8737 (mt-10) REVERT: W 98 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7275 (mpt) REVERT: X 98 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8411 (pt) REVERT: Y 62 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8583 (m) REVERT: Z 25 GLU cc_start: 0.8165 (pp20) cc_final: 0.7947 (pm20) REVERT: Z 85 GLU cc_start: 0.5507 (tt0) cc_final: 0.5003 (tt0) REVERT: a 58 LYS cc_start: 0.9045 (mtmp) cc_final: 0.8653 (mtpp) REVERT: b 99 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: c 34 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8129 (mmmt) REVERT: d 73 ASP cc_start: 0.8544 (p0) cc_final: 0.8340 (p0) REVERT: g 27 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8241 (mttm) REVERT: h 13 ASP cc_start: 0.9203 (t0) cc_final: 0.8889 (t0) REVERT: h 16 ARG cc_start: 0.8577 (mtm180) cc_final: 0.8279 (mtm180) REVERT: h 65 GLU cc_start: 0.9139 (tp30) cc_final: 0.8851 (tm-30) REVERT: l 111 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8635 (t70) REVERT: l 355 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8718 (t70) REVERT: m 77 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: m 81 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: m 139 GLU cc_start: 0.8582 (tt0) cc_final: 0.8324 (tt0) REVERT: n 30 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7639 (mtp180) REVERT: o 111 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8303 (mtmt) REVERT: p 42 CYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8246 (m) REVERT: v 53 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8773 (tp) REVERT: w 120 ASP cc_start: 0.8463 (t70) cc_final: 0.8131 (t70) REVERT: w 227 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7806 (mpt) REVERT: w 287 ASP cc_start: 0.7324 (t0) cc_final: 0.6988 (t0) outliers start: 113 outliers final: 55 residues processed: 713 average time/residue: 0.7829 time to fit residues: 665.5115 Evaluate side-chains 709 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 642 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain e residue 62 GLU Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 355 ASP Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 306 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 352 optimal weight: 5.9990 chunk 383 optimal weight: 0.0170 chunk 39 optimal weight: 0.0980 chunk 117 optimal weight: 3.9990 chunk 337 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 375 optimal weight: 0.9980 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN U 83 ASN ** a 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN g 18 ASN h 21 GLN i 319 HIS l 109 HIS n 3 ASN r 139 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.078006 restraints weight = 57318.682| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.77 r_work: 0.2741 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40693 Z= 0.129 Angle : 0.535 9.586 54897 Z= 0.270 Chirality : 0.040 0.215 5931 Planarity : 0.004 0.062 6676 Dihedral : 16.463 167.322 6667 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 2.82 % Allowed : 15.51 % Favored : 81.67 % 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 (0.13), residues: 4666 helix: 2.32 (0.09), residues: 2961 sheet: -1.59 (0.80), residues: 35 loop : -0.66 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG w 72 TYR 0.021 0.001 TYR l 587 PHE 0.029 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00298 (40683) covalent geometry : angle 0.53431 (54881) SS BOND : bond 0.00287 ( 8) SS BOND : angle 1.42654 ( 16) hydrogen bonds : bond 0.04699 ( 2294) hydrogen bonds : angle 3.95775 ( 6684) Misc. bond : bond 0.00456 ( 2) *********************** 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 776 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 660 time to evaluate : 1.445 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 56 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.5812 (mmtt) REVERT: S 4 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8703 (mt-10) REVERT: U 62 ASN cc_start: 0.8299 (t0) cc_final: 0.7985 (t160) REVERT: W 98 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7298 (mpt) REVERT: X 98 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8396 (pt) REVERT: X 155 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.6292 (m-10) REVERT: Y 62 SER cc_start: 0.8769 (m) cc_final: 0.8548 (m) REVERT: Z 85 GLU cc_start: 0.5549 (tt0) cc_final: 0.4975 (tt0) REVERT: b 24 LYS cc_start: 0.9042 (tptt) cc_final: 0.8805 (tptt) REVERT: b 99 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: c 34 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8134 (mmmt) REVERT: d 73 ASP cc_start: 0.8558 (p0) cc_final: 0.8339 (p0) REVERT: g 27 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8260 (mttm) REVERT: h 16 ARG cc_start: 0.8566 (mtm180) cc_final: 0.8212 (mtm110) REVERT: h 65 GLU cc_start: 0.9136 (tp30) cc_final: 0.8852 (tm-30) REVERT: j 1 MET cc_start: 0.7343 (tpp) cc_final: 0.7064 (tpp) REVERT: l 111 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8601 (t70) REVERT: l 579 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7893 (m-40) REVERT: m 77 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: n 30 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7579 (mtp180) REVERT: o 111 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8316 (mtmt) REVERT: r 340 ARG cc_start: 0.8938 (mtm110) cc_final: 0.8727 (mtm-85) REVERT: s 62 ARG cc_start: 0.8398 (ptt90) cc_final: 0.8181 (ptm160) REVERT: s 70 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8689 (mtm) REVERT: v 53 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8690 (tp) REVERT: w 51 ARG cc_start: 0.8493 (ptp-170) cc_final: 0.8250 (mtm-85) REVERT: w 72 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7562 (ttp80) REVERT: w 120 ASP cc_start: 0.8504 (t70) cc_final: 0.8191 (t70) REVERT: w 227 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8271 (mpp) REVERT: w 287 ASP cc_start: 0.7328 (t0) cc_final: 0.6933 (t0) outliers start: 116 outliers final: 57 residues processed: 712 average time/residue: 0.7749 time to fit residues: 659.1226 Evaluate side-chains 707 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 638 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain U residue 11 ASN Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain e residue 62 GLU Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 579 ASN Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 244 MET Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 70 MET Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 313 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 324 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 226 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN ** a 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN e 148 GLN g 18 ASN i 319 HIS l 109 HIS l 135 ASN l 199 GLN n 3 ASN r 251 ASN r 304 GLN v 65 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.098203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.078607 restraints weight = 57387.115| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.77 r_work: 0.2749 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40693 Z= 0.123 Angle : 0.532 8.764 54897 Z= 0.268 Chirality : 0.040 0.227 5931 Planarity : 0.004 0.061 6676 Dihedral : 15.888 169.406 6667 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.48 % Allowed : 16.14 % Favored : 81.38 % 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: 1.96 (0.13), residues: 4666 helix: 2.37 (0.09), residues: 2955 sheet: -1.62 (0.81), residues: 35 loop : -0.63 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 59 TYR 0.021 0.001 TYR l 587 PHE 0.029 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00280 (40683) covalent geometry : angle 0.53159 (54881) SS BOND : bond 0.00482 ( 8) SS BOND : angle 1.36723 ( 16) hydrogen bonds : bond 0.04525 ( 2294) hydrogen bonds : angle 3.92240 ( 6684) Misc. bond : bond 0.00270 ( 2) *********************** 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 763 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 661 time to evaluate : 1.549 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 62 ASN cc_start: 0.8316 (t0) cc_final: 0.7998 (t160) REVERT: U 79 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8371 (mm-30) REVERT: W 98 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7282 (mpt) REVERT: X 98 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8381 (pt) REVERT: Y 62 SER cc_start: 0.8761 (m) cc_final: 0.8539 (m) REVERT: Z 25 GLU cc_start: 0.8219 (pp20) cc_final: 0.7952 (pm20) REVERT: Z 85 GLU cc_start: 0.5534 (tt0) cc_final: 0.4969 (tt0) REVERT: a 58 LYS cc_start: 0.9038 (mtmp) cc_final: 0.8650 (mtpp) REVERT: b 99 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: c 34 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8136 (mmmt) REVERT: d 73 ASP cc_start: 0.8537 (p0) cc_final: 0.8289 (p0) REVERT: g 19 GLU cc_start: 0.8126 (tt0) cc_final: 0.7660 (pt0) REVERT: g 27 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8252 (mttm) REVERT: g 113 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: h 16 ARG cc_start: 0.8579 (mtm180) cc_final: 0.8218 (mtm110) REVERT: h 65 GLU cc_start: 0.9127 (tp30) cc_final: 0.8842 (tm-30) REVERT: j 1 MET cc_start: 0.7311 (tpp) cc_final: 0.7019 (tpp) REVERT: l 111 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8589 (t70) REVERT: l 579 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7933 (m-40) REVERT: m 1 MET cc_start: 0.2917 (tpt) cc_final: 0.2001 (ptt) REVERT: m 77 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: n 30 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7577 (mtp180) REVERT: o 111 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8333 (mtmt) REVERT: p 70 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: r 340 ARG cc_start: 0.8870 (mtm110) cc_final: 0.8646 (mtm-85) REVERT: s 62 ARG cc_start: 0.8366 (ptt90) cc_final: 0.8119 (ptm160) REVERT: v 53 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8653 (tp) REVERT: w 51 ARG cc_start: 0.8472 (ptp-170) cc_final: 0.8253 (mtm-85) REVERT: w 72 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7577 (ttp80) REVERT: w 120 ASP cc_start: 0.8505 (t70) cc_final: 0.7925 (t70) REVERT: w 227 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8228 (mpp) REVERT: w 287 ASP cc_start: 0.7310 (t0) cc_final: 0.6957 (t0) outliers start: 102 outliers final: 51 residues processed: 712 average time/residue: 0.7892 time to fit residues: 673.5405 Evaluate side-chains 705 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 644 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 579 ASN Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 454 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 349 optimal weight: 1.9990 chunk 160 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 374 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 321 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN U 83 ASN a 189 ASN b 13 GLN g 18 ASN l 109 HIS n 3 ASN r 304 GLN v 65 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.080183 restraints weight = 57034.665| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.77 r_work: 0.2779 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 40693 Z= 0.110 Angle : 0.519 9.853 54897 Z= 0.261 Chirality : 0.039 0.216 5931 Planarity : 0.004 0.062 6676 Dihedral : 15.135 172.055 6667 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 2.23 % Allowed : 16.87 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.13), residues: 4666 helix: 2.45 (0.09), residues: 2955 sheet: -1.71 (0.80), residues: 35 loop : -0.58 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 59 TYR 0.021 0.001 TYR r 406 PHE 0.029 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00241 (40683) covalent geometry : angle 0.51919 (54881) SS BOND : bond 0.00485 ( 8) SS BOND : angle 1.11290 ( 16) hydrogen bonds : bond 0.04182 ( 2294) hydrogen bonds : angle 3.84965 ( 6684) Misc. bond : bond 0.00039 ( 2) *********************** 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 783 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 691 time to evaluate : 1.382 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 62 ASN cc_start: 0.8302 (t0) cc_final: 0.7969 (t160) REVERT: W 98 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7292 (mpt) REVERT: X 98 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8366 (pt) REVERT: Y 62 SER cc_start: 0.8734 (m) cc_final: 0.8519 (m) REVERT: Y 95 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8511 (tt0) REVERT: Z 14 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.5538 (pp-130) REVERT: Z 25 GLU cc_start: 0.8239 (pp20) cc_final: 0.7938 (tm-30) REVERT: Z 42 ARG cc_start: 0.8029 (ptm160) cc_final: 0.7743 (ptm160) REVERT: Z 49 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: Z 85 GLU cc_start: 0.5469 (tt0) cc_final: 0.4991 (tt0) REVERT: c 34 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8031 (mmmt) REVERT: d 73 ASP cc_start: 0.8538 (p0) cc_final: 0.8325 (p0) REVERT: f 73 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8626 (m110) REVERT: g 27 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8247 (mttm) REVERT: g 113 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: h 13 ASP cc_start: 0.9012 (t0) cc_final: 0.8796 (t0) REVERT: h 16 ARG cc_start: 0.8575 (mtm180) cc_final: 0.8244 (mtm110) REVERT: h 65 GLU cc_start: 0.9136 (tp30) cc_final: 0.8852 (tm-30) REVERT: i 49 ASN cc_start: 0.8078 (p0) cc_final: 0.7856 (p0) REVERT: j 1 MET cc_start: 0.7303 (tpp) cc_final: 0.7000 (tpp) REVERT: l 108 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8831 (mmm) REVERT: l 111 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8915 (t0) REVERT: m 1 MET cc_start: 0.2920 (OUTLIER) cc_final: 0.1976 (ptt) REVERT: m 128 TYR cc_start: 0.7950 (m-80) cc_final: 0.6654 (m-80) REVERT: n 30 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7548 (mtp180) REVERT: o 111 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8336 (mtmt) REVERT: p 70 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: r 222 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8301 (mm-30) REVERT: r 257 MET cc_start: 0.9071 (mmp) cc_final: 0.8852 (mmm) REVERT: r 294 MET cc_start: 0.8975 (mmp) cc_final: 0.8772 (mmm) REVERT: w 120 ASP cc_start: 0.8459 (t70) cc_final: 0.7883 (t70) REVERT: w 227 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8230 (mpp) REVERT: w 287 ASP cc_start: 0.7281 (t0) cc_final: 0.6962 (t0) outliers start: 92 outliers final: 45 residues processed: 736 average time/residue: 0.7691 time to fit residues: 679.4996 Evaluate side-chains 715 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 659 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 108 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 391 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 244 MET Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 346 optimal weight: 2.9990 chunk 287 optimal weight: 0.5980 chunk 421 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 408 optimal weight: 0.0870 chunk 252 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 423 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 414 optimal weight: 0.9980 chunk 429 optimal weight: 4.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 36 GLN U 11 ASN U 83 ASN a 189 ASN b 13 GLN e 148 GLN g 18 ASN l 109 HIS n 3 ASN r 304 GLN v 65 GLN ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.079192 restraints weight = 57253.398| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.77 r_work: 0.2763 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40693 Z= 0.127 Angle : 0.540 11.289 54897 Z= 0.270 Chirality : 0.040 0.212 5931 Planarity : 0.004 0.063 6676 Dihedral : 14.838 174.909 6667 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 2.16 % Allowed : 17.57 % Favored : 80.27 % 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: 2.05 (0.13), residues: 4666 helix: 2.43 (0.09), residues: 2955 sheet: -1.65 (0.82), residues: 35 loop : -0.56 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG w 72 TYR 0.022 0.001 TYR l 587 PHE 0.029 0.001 PHE i 292 TRP 0.018 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00297 (40683) covalent geometry : angle 0.53962 (54881) SS BOND : bond 0.00340 ( 8) SS BOND : angle 1.27514 ( 16) hydrogen bonds : bond 0.04397 ( 2294) hydrogen bonds : angle 3.87598 ( 6684) Misc. bond : bond 0.00062 ( 2) *********************** 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 751 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 662 time to evaluate : 1.457 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 56 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.5654 (mmtt) REVERT: U 62 ASN cc_start: 0.8270 (t0) cc_final: 0.7961 (t160) REVERT: W 98 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7251 (mpt) REVERT: X 98 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8398 (pt) REVERT: Y 62 SER cc_start: 0.8752 (m) cc_final: 0.8533 (m) REVERT: Y 95 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8476 (tt0) REVERT: Z 25 GLU cc_start: 0.8195 (pp20) cc_final: 0.7939 (tm-30) REVERT: Z 42 ARG cc_start: 0.8042 (ptm160) cc_final: 0.7757 (ptm160) REVERT: Z 49 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: Z 85 GLU cc_start: 0.5621 (tt0) cc_final: 0.5001 (tt0) REVERT: b 27 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8404 (mt-10) REVERT: b 99 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: c 34 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8019 (mmmt) REVERT: d 73 ASP cc_start: 0.8558 (p0) cc_final: 0.8351 (p0) REVERT: g 27 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8261 (mttm) REVERT: g 113 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: h 13 ASP cc_start: 0.9056 (t0) cc_final: 0.8835 (t0) REVERT: h 16 ARG cc_start: 0.8564 (mtm180) cc_final: 0.8282 (mtm110) REVERT: h 65 GLU cc_start: 0.9140 (tp30) cc_final: 0.8849 (tm-30) REVERT: h 102 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7060 (pt0) REVERT: i 100 MET cc_start: 0.8745 (mmm) cc_final: 0.8542 (mtp) REVERT: l 108 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8834 (mmm) REVERT: l 111 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8926 (t0) REVERT: m 1 MET cc_start: 0.2956 (OUTLIER) cc_final: 0.2079 (ptt) REVERT: m 77 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: m 81 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: m 128 TYR cc_start: 0.7963 (m-80) cc_final: 0.6623 (m-80) REVERT: n 30 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7511 (mtt-85) REVERT: o 111 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8329 (mtmt) REVERT: r 257 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8917 (mmm) REVERT: s 70 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8564 (mtm) REVERT: w 72 ARG cc_start: 0.8056 (ttp-110) cc_final: 0.7542 (ttp80) REVERT: w 120 ASP cc_start: 0.8502 (t70) cc_final: 0.7943 (t70) REVERT: w 227 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8221 (mpp) REVERT: w 287 ASP cc_start: 0.7352 (t0) cc_final: 0.7105 (t0) REVERT: w 288 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7822 (t0) outliers start: 89 outliers final: 50 residues processed: 706 average time/residue: 0.7730 time to fit residues: 651.5605 Evaluate side-chains 712 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 646 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain U residue 11 ASN Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 108 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 391 SER Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 257 MET Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 70 MET Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 VAL Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 287 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 387 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 375 optimal weight: 2.9990 chunk 368 optimal weight: 2.9990 chunk 393 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 299 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 36 GLN U 11 ASN U 83 ASN ** a 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN g 18 ASN l 109 HIS l 135 ASN l 199 GLN n 3 ASN r 304 GLN v 65 GLN ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.099013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.079406 restraints weight = 57948.473| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.79 r_work: 0.2757 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40693 Z= 0.146 Angle : 0.560 12.768 54897 Z= 0.280 Chirality : 0.041 0.221 5931 Planarity : 0.004 0.064 6676 Dihedral : 14.702 179.185 6667 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 2.06 % Allowed : 17.65 % Favored : 80.29 % 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: 2.01 (0.13), residues: 4666 helix: 2.37 (0.09), residues: 2963 sheet: -1.60 (0.82), residues: 35 loop : -0.54 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG w 72 TYR 0.023 0.001 TYR l 587 PHE 0.030 0.001 PHE i 292 TRP 0.018 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00348 (40683) covalent geometry : angle 0.55976 (54881) SS BOND : bond 0.00370 ( 8) SS BOND : angle 1.32718 ( 16) hydrogen bonds : bond 0.04673 ( 2294) hydrogen bonds : angle 3.90800 ( 6684) Misc. bond : bond 0.00074 ( 2) *********************** 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 737 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 652 time to evaluate : 1.484 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 56 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.5634 (mmtt) REVERT: U 62 ASN cc_start: 0.8293 (t0) cc_final: 0.7972 (t160) REVERT: W 98 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7239 (mpt) REVERT: X 98 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8377 (pt) REVERT: Y 62 SER cc_start: 0.8777 (m) cc_final: 0.8545 (m) REVERT: Y 95 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8427 (tt0) REVERT: Z 42 ARG cc_start: 0.8008 (ptm160) cc_final: 0.7724 (ptm160) REVERT: Z 85 GLU cc_start: 0.5719 (tt0) cc_final: 0.5082 (tt0) REVERT: b 27 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8396 (mt-10) REVERT: b 99 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: c 34 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8012 (mmmt) REVERT: d 73 ASP cc_start: 0.8567 (p0) cc_final: 0.8362 (p0) REVERT: g 27 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8221 (mttm) REVERT: h 16 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8229 (mtm110) REVERT: h 65 GLU cc_start: 0.9152 (tp30) cc_final: 0.8851 (tm-30) REVERT: h 102 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7035 (pt0) REVERT: l 108 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8925 (mmm) REVERT: l 111 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8923 (t0) REVERT: m 1 MET cc_start: 0.2930 (OUTLIER) cc_final: 0.2076 (ptt) REVERT: m 77 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: m 81 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: m 128 TYR cc_start: 0.7933 (m-80) cc_final: 0.6528 (m-80) REVERT: n 30 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7567 (mtt-85) REVERT: o 111 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8264 (mtmt) REVERT: r 257 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8793 (mmm) REVERT: s 70 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8573 (mtm) REVERT: v 53 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8678 (tp) REVERT: w 72 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7570 (ttp80) REVERT: w 120 ASP cc_start: 0.8524 (t70) cc_final: 0.7976 (t70) REVERT: w 227 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8180 (mpp) REVERT: w 287 ASP cc_start: 0.7320 (t0) cc_final: 0.7067 (t0) REVERT: w 288 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7753 (t0) outliers start: 85 outliers final: 53 residues processed: 693 average time/residue: 0.7635 time to fit residues: 631.6499 Evaluate side-chains 720 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 652 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain U residue 11 ASN Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 108 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 257 MET Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 70 MET Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 328 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 393 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 339 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 387 optimal weight: 4.9990 chunk 365 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 36 GLN U 11 ASN U 83 ASN ** a 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN e 148 GLN g 18 ASN l 109 HIS l 135 ASN l 199 GLN n 3 ASN r 304 GLN v 65 GLN ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.079675 restraints weight = 57671.884| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.79 r_work: 0.2763 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40693 Z= 0.135 Angle : 0.556 12.318 54897 Z= 0.278 Chirality : 0.041 0.221 5931 Planarity : 0.004 0.064 6676 Dihedral : 14.519 176.896 6667 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.25 % Rotamer: Outliers : 1.89 % Allowed : 17.99 % Favored : 80.12 % 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: 2.01 (0.13), residues: 4666 helix: 2.37 (0.09), residues: 2963 sheet: -1.61 (0.82), residues: 35 loop : -0.53 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG w 72 TYR 0.022 0.001 TYR l 587 PHE 0.029 0.001 PHE i 292 TRP 0.018 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00317 (40683) covalent geometry : angle 0.55526 (54881) SS BOND : bond 0.00350 ( 8) SS BOND : angle 1.23880 ( 16) hydrogen bonds : bond 0.04587 ( 2294) hydrogen bonds : angle 3.89357 ( 6684) Misc. bond : bond 0.00063 ( 2) ********************** 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 735 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 657 time to evaluate : 1.463 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 56 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.5635 (mmtt) REVERT: U 62 ASN cc_start: 0.8317 (t0) cc_final: 0.8013 (t160) REVERT: W 98 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7166 (mpt) REVERT: X 98 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8404 (pt) REVERT: Y 62 SER cc_start: 0.8769 (m) cc_final: 0.8531 (m) REVERT: Y 95 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8426 (tt0) REVERT: Z 25 GLU cc_start: 0.8289 (pp20) cc_final: 0.7992 (tm-30) REVERT: Z 42 ARG cc_start: 0.8006 (ptm160) cc_final: 0.7723 (ptm160) REVERT: Z 85 GLU cc_start: 0.5700 (tt0) cc_final: 0.5083 (tt0) REVERT: b 27 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8388 (mt-10) REVERT: b 99 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: c 34 LYS cc_start: 0.8375 (mmmt) cc_final: 0.7979 (mmmt) REVERT: g 27 LYS cc_start: 0.8578 (mtmm) cc_final: 0.8207 (mttm) REVERT: h 16 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8229 (mtm110) REVERT: h 65 GLU cc_start: 0.9159 (tp30) cc_final: 0.8859 (tm-30) REVERT: h 102 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7019 (pt0) REVERT: i 100 MET cc_start: 0.8628 (mtp) cc_final: 0.8296 (mtp) REVERT: i 336 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8335 (t) REVERT: l 108 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8910 (mmm) REVERT: l 111 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8940 (t0) REVERT: m 1 MET cc_start: 0.3047 (OUTLIER) cc_final: 0.2286 (ptt) REVERT: m 77 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: m 81 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: m 128 TYR cc_start: 0.7925 (m-80) cc_final: 0.6530 (m-80) REVERT: n 30 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7536 (mtt-85) REVERT: o 111 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8257 (mtmt) REVERT: r 222 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8352 (mm-30) REVERT: r 257 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8781 (mmm) REVERT: s 62 ARG cc_start: 0.8277 (ptm160) cc_final: 0.8060 (ptm-80) REVERT: s 70 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8557 (mtm) REVERT: v 53 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8632 (tp) REVERT: w 72 ARG cc_start: 0.8087 (ttp-110) cc_final: 0.7560 (ttp80) REVERT: w 120 ASP cc_start: 0.8519 (t70) cc_final: 0.7933 (t70) REVERT: w 227 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8176 (mpp) REVERT: w 287 ASP cc_start: 0.7302 (t0) cc_final: 0.7053 (t0) REVERT: w 288 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7834 (t0) outliers start: 78 outliers final: 52 residues processed: 694 average time/residue: 0.7904 time to fit residues: 660.6122 Evaluate side-chains 718 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 650 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain U residue 11 ASN Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 108 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain m residue 170 GLU Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 257 MET Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 70 MET Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 6 optimal weight: 0.6980 chunk 384 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 381 optimal weight: 0.0030 chunk 88 optimal weight: 0.7980 chunk 435 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 36 GLN U 11 ASN U 83 ASN a 189 ASN b 13 GLN g 18 ASN l 109 HIS n 3 ASN r 304 GLN v 65 GLN ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.081441 restraints weight = 57657.606| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.80 r_work: 0.2801 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40693 Z= 0.114 Angle : 0.541 11.143 54897 Z= 0.271 Chirality : 0.040 0.212 5931 Planarity : 0.004 0.062 6676 Dihedral : 14.159 172.030 6667 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 1.82 % Allowed : 18.18 % Favored : 80.00 % 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: 2.42 (0.09), residues: 2965 sheet: -1.63 (0.81), residues: 35 loop : -0.50 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG w 72 TYR 0.021 0.001 TYR r 406 PHE 0.029 0.001 PHE i 292 TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00254 (40683) covalent geometry : angle 0.54112 (54881) SS BOND : bond 0.00291 ( 8) SS BOND : angle 1.19277 ( 16) hydrogen bonds : bond 0.04187 ( 2294) hydrogen bonds : angle 3.83588 ( 6684) Misc. bond : bond 0.00042 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15670.92 seconds wall clock time: 266 minutes 32.99 seconds (15992.99 seconds total)