Starting phenix.real_space_refine on Sat Mar 7 08:25:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vy9_32197/03_2026/7vy9_32197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vy9_32197/03_2026/7vy9_32197.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 { model { file = "/net/cci-nas-00/data/ceres_data/7vy9_32197/03_2026/7vy9_32197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vy9_32197/03_2026/7vy9_32197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vy9_32197/03_2026/7vy9_32197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vy9_32197/03_2026/7vy9_32197.map" } 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= 0.005 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 36 5.49 5 S 294 5.16 5 C 26110 2.51 5 N 6289 2.21 5 O 6988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s 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: 39717 Number of models: 1 Model: "" Number of chains: 42 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: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 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: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "m" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1295 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1059 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 336 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "n" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "r" Number of atoms: 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: "s" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 219 Unusual residues: {' UQ': 1, 'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "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: 8.86, per 1000 atoms: 0.22 Number of scatterers: 39717 At special positions: 0 Unit cell: (182.614, 190.133, 138.572, 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 294 16.00 P 36 15.00 O 6988 8.00 N 6289 7.00 C 26110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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 u 46 " - pdb=" SG CYS u 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8954 Finding SS restraints... Secondary structure from input PDB file: 219 helices and 6 sheets defined 70.5% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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 'S' and resid 1 through 4 Processing helix chain 'S' and resid 5 through 30 removed outlier: 3.656A 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: 3.857A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.937A pdb=" N ASP S 70 " --> pdb=" O GLU S 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 16 removed outlier: 3.733A pdb=" N SER U 7 " --> pdb=" O GLY U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 32 Processing helix chain 'U' and resid 33 through 36 Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 78 through 84 Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 17 through 44 Processing helix chain 'V' and resid 48 through 82 Processing helix chain 'V' and resid 86 through 106 removed outlier: 4.358A 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 99 through 101 No H-bonds generated for 'chain 'W' and resid 99 through 101' Processing helix chain 'W' and resid 129 through 143 removed outlier: 5.858A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 89 Processing helix chain 'X' and resid 111 through 127 Processing helix chain 'X' and resid 131 through 136 Processing helix chain 'X' and resid 140 through 152 Processing helix chain 'Y' and resid 51 through 76 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: 3.529A pdb=" N TRP Z 22 " --> pdb=" O TYR Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 38 removed outlier: 3.852A pdb=" N THR Z 31 " --> pdb=" O THR Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 55 removed outlier: 4.150A 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 Processing helix chain 'Z' and resid 88 through 90 No H-bonds generated for 'chain 'Z' and resid 88 through 90' Processing helix chain 'a' and resid 61 through 93 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 108 through 113 removed outlier: 3.793A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) removed outlier: 3.739A 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: 4.095A pdb=" N ASN a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 Processing helix chain 'b' and resid 5 through 26 Processing helix chain 'b' and resid 68 through 75 removed outlier: 3.819A 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 Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 82 through 86 Processing helix chain 'c' and resid 108 through 112 Processing helix chain 'c' and resid 128 through 150 Processing helix chain 'd' and resid 28 through 58 removed outlier: 4.463A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix removed outlier: 3.542A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 77 removed outlier: 3.631A pdb=" N CYS d 77 " --> pdb=" O ILE d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 118 removed outlier: 3.884A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 125 through 144 Processing helix chain 'd' and resid 151 through 175 Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.422A pdb=" N LYS e 69 " --> pdb=" O ASN e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 95 Processing helix chain 'e' and resid 97 through 108 Processing helix chain 'e' and resid 115 through 132 Processing helix chain 'e' and resid 143 through 147 Processing helix chain 'f' and resid 40 through 73 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: 3.738A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 103 Processing helix chain 'h' and resid 5 through 11 Processing helix chain 'h' and resid 15 through 19 Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 45 Processing helix chain 'h' and resid 48 through 56 removed outlier: 4.027A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 56 through 69 Processing helix chain 'h' and resid 69 through 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: 3.658A 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: 4.308A 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 171 removed outlier: 3.773A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 174 through 193 removed outlier: 3.906A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 197 through 222 removed outlier: 3.602A 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 Processing helix chain 'i' and resid 259 through 273 removed outlier: 4.272A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 3.649A pdb=" N THR i 280 " --> pdb=" O ILE i 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 3.703A pdb=" N LYS i 314 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 325 through 335 Processing helix chain 'i' and resid 336 through 347 Proline residue: i 341 - end of helix removed outlier: 3.814A 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: 3.612A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 80 removed outlier: 4.260A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 108 removed outlier: 3.717A pdb=" N MET j 87 " --> pdb=" O ASN j 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 21 removed outlier: 3.643A pdb=" N MET k 6 " --> pdb=" O PRO k 2 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 51 removed outlier: 3.844A pdb=" N SER k 29 " --> pdb=" O HIS k 25 " (cutoff:3.500A) 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: 4.599A pdb=" N ILE k 61 " --> pdb=" O ASN k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 94 through 98 removed outlier: 3.654A pdb=" N CYS k 98 " --> pdb=" O LEU k 95 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 14 removed outlier: 4.368A pdb=" N SER l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) removed outlier: 3.538A 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: 4.462A 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: 3.860A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 134 Processing helix chain 'l' and resid 136 through 156 Processing helix chain 'l' and resid 161 through 194 removed outlier: 3.865A 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: 4.224A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.758A 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 270 through 293 removed outlier: 3.536A pdb=" N GLN l 274 " --> pdb=" O ASN l 270 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 4.049A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 355 through 359 Processing helix chain 'l' and resid 366 through 381 Processing helix chain 'l' and resid 386 through 401 removed outlier: 3.585A pdb=" N TYR l 390 " --> pdb=" O LEU l 386 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 405 through 432 removed outlier: 3.686A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU l 432 " --> pdb=" O PHE l 428 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 470 removed outlier: 5.955A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.385A 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 508 removed outlier: 3.701A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) 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: 3.725A pdb=" N LEU l 562 " --> pdb=" O LEU l 558 " (cutoff:3.500A) Processing helix chain 'l' and resid 562 through 579 Processing helix chain 'l' and resid 583 through 602 removed outlier: 3.522A 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 24 through 46 removed outlier: 4.193A pdb=" N TYR m 28 " --> pdb=" O PRO m 24 " (cutoff:3.500A) 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 149 removed outlier: 4.070A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER m 148 " --> pdb=" O ALA m 144 " (cutoff:3.500A) 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 19 through 23 Processing helix chain 'o' and resid 26 through 52 removed outlier: 3.802A 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: 4.392A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 75 Processing helix chain 'p' and resid 94 through 98 removed outlier: 3.576A pdb=" N LYS p 98 " --> pdb=" O GLU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 100 through 107 Processing helix chain 'p' and resid 108 through 114 removed outlier: 3.844A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 143 removed outlier: 3.505A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.866A 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 18 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: 3.647A 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 84 removed outlier: 4.007A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.396A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 88 through 112 removed outlier: 3.653A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 125 through 137 removed outlier: 3.796A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 172 removed outlier: 3.602A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 175 through 182 Processing helix chain 'r' and resid 189 through 207 removed outlier: 4.545A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 3.979A 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: 4.252A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU r 250 " --> pdb=" O ILE r 246 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN r 251 " --> pdb=" O THR r 247 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 276 removed outlier: 5.316A pdb=" N TYR r 259 " --> pdb=" O ASN r 255 " (cutoff:3.500A) Proline residue: r 260 - end of helix Processing helix chain 'r' and resid 277 through 279 No H-bonds generated for 'chain 'r' and resid 277 through 279' Processing helix chain 'r' and resid 281 through 304 Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.543A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 347 through 352 removed outlier: 4.318A pdb=" N LEU r 351 " --> pdb=" O GLY r 347 " (cutoff:3.500A) Processing helix chain 'r' and resid 352 through 367 Processing helix chain 'r' and resid 372 through 389 Processing helix chain 'r' and resid 391 through 416 removed outlier: 4.131A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR r 409 " --> pdb=" O LEU r 405 " (cutoff:3.500A) Processing helix chain 'r' and resid 430 through 450 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 451 through 455 removed outlier: 3.592A 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: 3.703A 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 58 Processing helix chain 's' and resid 67 through 85 Proline residue: s 75 - end of helix Processing helix chain 's' and resid 100 through 123 removed outlier: 3.566A pdb=" N PHE s 104 " --> pdb=" O LEU s 100 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 158 removed outlier: 5.095A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN s 157 " --> pdb=" O VAL s 153 " (cutoff:3.500A) Processing helix chain 's' and resid 161 through 169 removed outlier: 3.897A pdb=" N LEU s 165 " --> pdb=" O THR s 161 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE s 166 " --> pdb=" O LEU s 162 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 177 Processing helix chain 's' and resid 178 through 193 Processing helix chain 's' and resid 209 through 213 removed outlier: 3.999A pdb=" N ASN s 212 " --> pdb=" O SER s 209 " (cutoff:3.500A) Processing helix chain 's' and resid 216 through 243 removed outlier: 3.839A pdb=" N PHE s 220 " --> pdb=" O ALA s 216 " (cutoff:3.500A) Processing helix chain 's' and resid 252 through 277 Processing helix chain 's' and resid 281 through 292 Processing helix chain 's' and resid 292 through 312 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 9 through 14 removed outlier: 3.545A pdb=" N LYS u 14 " --> pdb=" O GLU u 11 " (cutoff:3.500A) Processing helix chain 'u' and resid 21 through 36 removed outlier: 4.869A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 51 removed outlier: 3.530A pdb=" N ASN u 40 " --> pdb=" O CYS u 36 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 55 Processing helix chain 'u' and resid 56 through 78 Processing helix chain 'u' and resid 79 through 92 removed outlier: 3.767A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 114 Processing helix chain 'v' and resid 3 through 11 Processing helix chain 'v' and resid 12 through 16 Processing helix chain 'v' and resid 42 through 50 Processing helix chain 'v' and resid 59 through 73 removed outlier: 3.557A pdb=" N LEU v 63 " --> pdb=" O CYS v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 124 Processing helix chain 'w' and resid 39 through 45 Processing helix chain 'w' and resid 69 through 82 Processing helix chain 'w' and resid 92 through 97 removed outlier: 3.627A pdb=" N SER w 96 " --> pdb=" O HIS w 92 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 92 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 176 removed outlier: 4.651A pdb=" N PHE w 167 " --> pdb=" O ILE w 163 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL w 168 " --> pdb=" O TYR w 164 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE w 169 " --> pdb=" O SER w 165 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN w 176 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 196 removed outlier: 4.130A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) Processing helix chain 'w' and resid 210 through 222 removed outlier: 4.017A pdb=" N GLY w 222 " --> pdb=" O ILE w 218 " (cutoff:3.500A) Processing helix chain 'w' and resid 225 through 229 Processing helix chain 'w' and resid 230 through 244 removed outlier: 3.619A pdb=" N LEU w 234 " --> pdb=" O THR w 230 " (cutoff:3.500A) Processing helix chain 'w' and resid 244 through 251 removed outlier: 4.017A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 260 through 264 removed outlier: 4.272A pdb=" N GLU w 264 " --> pdb=" O ALA w 260 " (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: 3.698A pdb=" N VAL w 269 " --> pdb=" O ASP w 265 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR w 275 " --> pdb=" O GLU w 271 " (cutoff:3.500A) Processing helix chain 'w' and resid 282 through 286 Processing helix chain 'w' and resid 287 through 299 removed outlier: 3.544A pdb=" N GLN w 299 " --> pdb=" O ARG w 295 " (cutoff:3.500A) Processing helix chain 'w' and resid 300 through 306 Processing helix chain 'w' and resid 307 through 310 removed outlier: 3.844A pdb=" N ILE w 310 " --> pdb=" O TYR w 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 307 through 310' Processing helix chain 'w' and resid 320 through 333 Processing helix chain 'w' and resid 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: 6.046A 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: 5.276A 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: 5.366A pdb=" N SER l 64 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE l 80 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP l 66 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU l 76 " --> pdb=" O TRP l 68 " (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: 6.366A pdb=" N ARG w 84 " --> pdb=" O VAL w 158 " (cutoff:3.500A) 2336 hydrogen bonds defined for protein. 6786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 5.06 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: 5988 1.31 - 1.44: 10990 1.44 - 1.56: 22982 1.56 - 1.69: 235 1.69 - 1.82: 531 Bond restraints: 40726 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C18 UQ s 404 " pdb=" C19 UQ s 404 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C13 UQ s 404 " pdb=" C14 UQ s 404 " ideal model delta sigma weight residual 1.335 1.547 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C23 UQ s 404 " pdb=" C24 UQ s 404 " ideal model delta sigma weight residual 1.335 1.544 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C8 UQ s 404 " pdb=" C9 UQ s 404 " ideal model delta sigma weight residual 1.334 1.540 -0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 40721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 54299 3.44 - 6.87: 503 6.87 - 10.31: 99 10.31 - 13.74: 23 13.74 - 17.18: 12 Bond angle restraints: 54936 Sorted by residual: angle pdb=" N ILE l 26 " pdb=" CA ILE l 26 " pdb=" C ILE l 26 " ideal model delta sigma weight residual 113.71 106.88 6.83 9.50e-01 1.11e+00 5.16e+01 angle pdb=" C11 CDL V 201 " pdb=" CA5 CDL V 201 " pdb=" OA6 CDL V 201 " ideal model delta sigma weight residual 111.33 120.39 -9.06 1.32e+00 5.72e-01 4.69e+01 angle pdb=" C51 CDL V 202 " pdb=" CB5 CDL V 202 " pdb=" OB6 CDL V 202 " ideal model delta sigma weight residual 111.33 120.30 -8.97 1.32e+00 5.72e-01 4.60e+01 angle pdb=" C11 CDL s 402 " pdb=" CA5 CDL s 402 " pdb=" OA6 CDL s 402 " ideal model delta sigma weight residual 111.33 120.27 -8.94 1.32e+00 5.72e-01 4.57e+01 angle pdb=" C51 CDL s 402 " pdb=" CB5 CDL s 402 " pdb=" OB6 CDL s 402 " ideal model delta sigma weight residual 111.33 120.26 -8.93 1.32e+00 5.72e-01 4.56e+01 ... (remaining 54931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 23595 35.69 - 71.38: 1199 71.38 - 107.07: 81 107.07 - 142.76: 16 142.76 - 178.45: 19 Dihedral angle restraints: 24910 sinusoidal: 11050 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 -60.00 114.63 -174.63 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -132.57 46.57 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA TYR j 37 " pdb=" C TYR j 37 " pdb=" N GLU j 38 " pdb=" CA GLU j 38 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 24907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5301 0.066 - 0.132: 587 0.132 - 0.197: 28 0.197 - 0.263: 6 0.263 - 0.329: 9 Chirality restraints: 5931 Sorted by residual: chirality pdb=" C6 PLX a 202 " pdb=" C7 PLX a 202 " pdb=" O6 PLX a 202 " pdb=" O7 PLX a 202 " both_signs ideal model delta sigma weight residual False 2.01 2.34 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA TYR m 60 " pdb=" N TYR m 60 " pdb=" C TYR m 60 " pdb=" CB TYR m 60 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C6 PLX j 202 " pdb=" C7 PLX j 202 " pdb=" O6 PLX j 202 " pdb=" O7 PLX j 202 " both_signs ideal model delta sigma weight residual False 2.01 2.34 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 5928 not shown) Planarity restraints: 6684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 404 " 0.403 2.00e-02 2.50e+03 3.60e-01 1.62e+03 pdb=" C18 UQ s 404 " -0.409 2.00e-02 2.50e+03 pdb=" C19 UQ s 404 " -0.398 2.00e-02 2.50e+03 pdb=" C20 UQ s 404 " 0.003 2.00e-02 2.50e+03 pdb=" C21 UQ s 404 " 0.401 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 404 " -0.070 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C11 UQ s 404 " 0.071 2.00e-02 2.50e+03 pdb=" C7 UQ s 404 " -0.277 2.00e-02 2.50e+03 pdb=" C8 UQ s 404 " 0.519 2.00e-02 2.50e+03 pdb=" C9 UQ s 404 " -0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 404 " -0.122 2.00e-02 2.50e+03 1.84e-01 4.23e+02 pdb=" C13 UQ s 404 " 0.050 2.00e-02 2.50e+03 pdb=" C14 UQ s 404 " 0.330 2.00e-02 2.50e+03 pdb=" C15 UQ s 404 " -0.060 2.00e-02 2.50e+03 pdb=" C16 UQ s 404 " -0.198 2.00e-02 2.50e+03 ... (remaining 6681 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2905 2.74 - 3.28: 38916 3.28 - 3.82: 68462 3.82 - 4.36: 82896 4.36 - 4.90: 141575 Nonbonded interactions: 334754 Sorted by model distance: nonbonded pdb=" O LEU m 61 " pdb=" OH TYR s 114 " model vdw 2.198 3.040 nonbonded pdb=" OE1 GLU s 24 " pdb=" OH TYR s 228 " model vdw 2.200 3.040 nonbonded pdb=" O LEU j 73 " pdb=" OH TYR s 160 " model vdw 2.200 3.040 nonbonded pdb=" NH2 ARG W 81 " pdb=" OD1 ASN u 64 " model vdw 2.202 3.120 nonbonded pdb=" O LEU i 19 " pdb=" OG SER i 23 " model vdw 2.221 3.040 ... (remaining 334749 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: 2.620 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: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 35.470 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.226 40734 Z= 0.448 Angle : 0.863 17.181 54950 Z= 0.425 Chirality : 0.043 0.329 5931 Planarity : 0.008 0.360 6684 Dihedral : 19.863 178.447 15935 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 0.99 % Allowed : 15.01 % Favored : 84.00 % 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: 1.79 (0.12), residues: 4666 helix: 2.13 (0.10), residues: 2936 sheet: -0.66 (0.96), residues: 35 loop : -0.47 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG V 106 TYR 0.024 0.001 TYR i 208 PHE 0.028 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS S 27 Details of bonding type rmsd covalent geometry : bond 0.00785 (40726) covalent geometry : angle 0.86261 (54936) SS BOND : bond 0.00208 ( 7) SS BOND : angle 1.48578 ( 14) hydrogen bonds : bond 0.13222 ( 2336) hydrogen bonds : angle 5.49009 ( 6786) Misc. bond : bond 0.21830 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 690 time to evaluate : 1.468 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 123 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8518 (mt-10) REVERT: c 149 ILE cc_start: 0.8566 (pp) cc_final: 0.8348 (pt) REVERT: e 111 ASP cc_start: 0.7480 (t70) cc_final: 0.7109 (t70) REVERT: e 115 GLN cc_start: 0.7820 (pt0) cc_final: 0.7564 (pt0) REVERT: i 208 TYR cc_start: 0.9151 (t80) cc_final: 0.8758 (t80) REVERT: j 66 ASP cc_start: 0.8830 (t0) cc_final: 0.8626 (t0) REVERT: l 383 MET cc_start: 0.8962 (tpp) cc_final: 0.8724 (tpt) REVERT: m 64 MET cc_start: 0.9357 (mmp) cc_final: 0.9023 (mmp) REVERT: o 111 LYS cc_start: 0.8721 (mtpp) cc_final: 0.7988 (mttt) REVERT: r 398 MET cc_start: 0.8349 (mmm) cc_final: 0.7659 (ttm) REVERT: u 88 CYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6623 (t) REVERT: w 241 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.7212 (t80) outliers start: 41 outliers final: 23 residues processed: 714 average time/residue: 0.7947 time to fit residues: 676.3309 Evaluate side-chains 697 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 672 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain l residue 446 ASN Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN Z 60 ASN b 13 GLN i 47 ASN i 171 ASN k 50 ASN l 446 ASN l 580 GLN o 126 ASN p 12 HIS p 13 GLN p 53 ASN r 304 GLN u 77 HIS v 54 GLN w 107 GLN w 132 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.088577 restraints weight = 52600.104| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.26 r_work: 0.2784 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40734 Z= 0.165 Angle : 0.590 9.187 54950 Z= 0.297 Chirality : 0.042 0.191 5931 Planarity : 0.005 0.066 6684 Dihedral : 18.450 179.691 6710 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 2.72 % Allowed : 13.28 % Favored : 84.00 % 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: 1.89 (0.12), residues: 4666 helix: 2.13 (0.09), residues: 2983 sheet: -0.70 (1.14), residues: 25 loop : -0.33 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 106 TYR 0.024 0.001 TYR r 406 PHE 0.029 0.001 PHE i 292 TRP 0.022 0.001 TRP u 86 HIS 0.008 0.001 HIS S 27 Details of bonding type rmsd covalent geometry : bond 0.00387 (40726) covalent geometry : angle 0.58961 (54936) SS BOND : bond 0.00273 ( 7) SS BOND : angle 1.52998 ( 14) hydrogen bonds : bond 0.05457 ( 2336) hydrogen bonds : angle 4.34151 ( 6786) Misc. bond : bond 0.00350 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 694 time to evaluate : 1.577 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 48 MET cc_start: 0.9146 (mtp) cc_final: 0.8836 (mtm) REVERT: U 82 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8807 (tttt) REVERT: Y 91 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7969 (tm-30) REVERT: Z 30 GLU cc_start: 0.8324 (tt0) cc_final: 0.8053 (mt-10) REVERT: Z 49 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: a 76 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8855 (mp) REVERT: b 9 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8126 (mtpp) REVERT: b 93 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8072 (mttt) REVERT: c 74 ASP cc_start: 0.7920 (t0) cc_final: 0.7635 (t0) REVERT: c 149 ILE cc_start: 0.8727 (pp) cc_final: 0.8495 (pt) REVERT: h 5 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8268 (t0) REVERT: h 13 ASP cc_start: 0.8460 (t0) cc_final: 0.7948 (t0) REVERT: i 245 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8789 (tmm) REVERT: l 383 MET cc_start: 0.8913 (tpp) cc_final: 0.8620 (tpt) REVERT: m 64 MET cc_start: 0.9324 (mmp) cc_final: 0.8943 (mmp) REVERT: m 99 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7525 (ttm) REVERT: o 61 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: o 111 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8070 (mttt) REVERT: r 398 MET cc_start: 0.8437 (mmm) cc_final: 0.7866 (ttm) REVERT: s 227 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8356 (tp30) REVERT: u 37 ASP cc_start: 0.8490 (t0) cc_final: 0.8280 (t0) REVERT: u 155 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8032 (pp20) REVERT: w 241 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.7357 (t80) outliers start: 112 outliers final: 39 residues processed: 741 average time/residue: 0.8029 time to fit residues: 708.4784 Evaluate side-chains 722 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 673 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 245 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain o residue 61 GLU Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 403 optimal weight: 6.9990 chunk 357 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 408 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN U 62 ASN W 90 ASN Z 60 ASN b 13 GLN b 89 HIS e 148 GLN h 70 GLN i 47 ASN i 171 ASN k 50 ASN l 446 ASN l 580 GLN o 126 ASN r 304 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.089864 restraints weight = 52623.164| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.25 r_work: 0.2807 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 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 0.037 40734 Z= 0.126 Angle : 0.540 9.620 54950 Z= 0.272 Chirality : 0.040 0.178 5931 Planarity : 0.004 0.062 6684 Dihedral : 17.417 178.251 6686 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 2.84 % Allowed : 13.77 % Favored : 83.39 % 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 (0.12), residues: 4666 helix: 2.25 (0.09), residues: 2982 sheet: -0.47 (1.14), residues: 25 loop : -0.35 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 106 TYR 0.023 0.001 TYR r 406 PHE 0.028 0.001 PHE i 292 TRP 0.020 0.001 TRP u 86 HIS 0.005 0.001 HIS S 27 Details of bonding type rmsd covalent geometry : bond 0.00278 (40726) covalent geometry : angle 0.53983 (54936) SS BOND : bond 0.00829 ( 7) SS BOND : angle 1.36822 ( 14) hydrogen bonds : bond 0.04840 ( 2336) hydrogen bonds : angle 4.15736 ( 6786) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 713 time to evaluate : 1.447 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: S 48 MET cc_start: 0.9163 (mtp) cc_final: 0.8864 (mtm) REVERT: U 79 GLU cc_start: 0.7918 (tp30) cc_final: 0.7696 (mm-30) REVERT: X 125 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8020 (tm-30) REVERT: Z 30 GLU cc_start: 0.8407 (tt0) cc_final: 0.8158 (mt-10) REVERT: Z 49 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: b 9 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8130 (mtpp) REVERT: c 60 GLU cc_start: 0.8897 (mp0) cc_final: 0.8554 (mp0) REVERT: e 111 ASP cc_start: 0.7764 (t70) cc_final: 0.7213 (t0) REVERT: e 115 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: h 13 ASP cc_start: 0.8426 (t0) cc_final: 0.7839 (t0) REVERT: h 102 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: j 4 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8367 (mmt) REVERT: j 85 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8344 (mttt) REVERT: l 383 MET cc_start: 0.8917 (tpp) cc_final: 0.8639 (tpt) REVERT: m 77 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: m 99 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7473 (ttm) REVERT: s 206 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8311 (mp0) REVERT: s 227 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8360 (tp30) REVERT: s 296 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8886 (tt) REVERT: u 37 ASP cc_start: 0.8515 (t70) cc_final: 0.8254 (t0) REVERT: u 155 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8003 (pp20) REVERT: v 39 MET cc_start: 0.8255 (tpt) cc_final: 0.7873 (tpp) REVERT: v 48 ASP cc_start: 0.8408 (m-30) cc_final: 0.8171 (m-30) REVERT: w 241 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.7202 (t80) REVERT: w 251 GLU cc_start: 0.8004 (mp0) cc_final: 0.7401 (mp0) outliers start: 117 outliers final: 47 residues processed: 762 average time/residue: 0.7964 time to fit residues: 722.1143 Evaluate side-chains 737 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 679 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 4 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 492 ILE Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 342 optimal weight: 5.9990 chunk 435 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 370 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN Z 60 ASN b 13 GLN d 149 HIS f 61 GLN h 45 HIS h 70 GLN i 47 ASN ** i 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 186 HIS k 50 ASN l 534 HIS ** l 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 79 ASN o 126 ASN r 43 ASN r 251 ASN s 230 ASN u 77 HIS v 54 GLN w 107 GLN w 235 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.103745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.083827 restraints weight = 52746.731| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.25 r_work: 0.2704 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 40734 Z= 0.277 Angle : 0.685 10.876 54950 Z= 0.345 Chirality : 0.048 0.213 5931 Planarity : 0.005 0.061 6684 Dihedral : 17.304 172.960 6681 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 3.78 % Allowed : 13.62 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.12), residues: 4666 helix: 1.80 (0.09), residues: 2982 sheet: -0.87 (1.00), residues: 35 loop : -0.51 (0.16), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG n 30 TYR 0.023 0.002 TYR X 85 PHE 0.026 0.002 PHE i 292 TRP 0.022 0.002 TRP u 86 HIS 0.015 0.002 HIS S 27 Details of bonding type rmsd covalent geometry : bond 0.00680 (40726) covalent geometry : angle 0.68421 (54936) SS BOND : bond 0.00676 ( 7) SS BOND : angle 2.24277 ( 14) hydrogen bonds : bond 0.06724 ( 2336) hydrogen bonds : angle 4.42133 ( 6786) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 696 time to evaluate : 1.381 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: S 48 MET cc_start: 0.9188 (mtp) cc_final: 0.8916 (mtm) REVERT: V 8 LYS cc_start: 0.8403 (mttt) cc_final: 0.8127 (mtmm) REVERT: V 26 THR cc_start: 0.9275 (t) cc_final: 0.9065 (m) REVERT: W 99 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7690 (tmmt) REVERT: Y 99 ILE cc_start: 0.7560 (mt) cc_final: 0.7072 (tt) REVERT: Z 30 GLU cc_start: 0.8484 (tt0) cc_final: 0.8192 (mt-10) REVERT: Z 49 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: a 114 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9067 (ptmm) REVERT: a 130 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8417 (pm20) REVERT: a 152 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8913 (ttmm) REVERT: b 9 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8166 (mtpp) REVERT: b 93 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8163 (mttt) REVERT: b 119 LEU cc_start: 0.8806 (mm) cc_final: 0.8587 (mm) REVERT: e 111 ASP cc_start: 0.7879 (t70) cc_final: 0.7238 (t0) REVERT: e 115 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: f 61 GLN cc_start: 0.8909 (tp40) cc_final: 0.8522 (tp-100) REVERT: h 13 ASP cc_start: 0.8543 (t0) cc_final: 0.8076 (t0) REVERT: h 102 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: i 245 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.9061 (ttp) REVERT: j 85 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8410 (mttt) REVERT: m 77 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: m 99 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7552 (ttm) REVERT: m 135 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8371 (t80) REVERT: n 8 VAL cc_start: 0.7163 (OUTLIER) cc_final: 0.6798 (p) REVERT: n 41 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8913 (mttm) REVERT: n 54 GLU cc_start: 0.7879 (pm20) cc_final: 0.7508 (mp0) REVERT: p 70 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: r 17 MET cc_start: 0.8952 (mmm) cc_final: 0.8733 (mmm) REVERT: r 302 MET cc_start: 0.9235 (mmp) cc_final: 0.8940 (mmp) REVERT: s 206 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8459 (mp0) REVERT: s 227 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: s 296 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.8994 (tt) REVERT: u 37 ASP cc_start: 0.8660 (t70) cc_final: 0.8337 (t0) REVERT: v 48 ASP cc_start: 0.8472 (m-30) cc_final: 0.8211 (m-30) REVERT: v 105 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7868 (tp30) REVERT: w 293 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7992 (ttp80) outliers start: 156 outliers final: 75 residues processed: 762 average time/residue: 0.7902 time to fit residues: 717.1172 Evaluate side-chains 765 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 671 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 99 LYS Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 245 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 170 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 85 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 374 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 331 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 324 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 430 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN U 62 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN b 13 GLN h 70 GLN i 47 ASN i 171 ASN k 50 ASN ** l 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 ASN u 77 HIS v 54 GLN v 117 GLN w 107 GLN 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 = 0.106519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.086798 restraints weight = 52368.921| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.24 r_work: 0.2750 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40734 Z= 0.162 Angle : 0.584 10.652 54950 Z= 0.296 Chirality : 0.042 0.189 5931 Planarity : 0.005 0.064 6684 Dihedral : 16.661 177.162 6681 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 3.13 % Allowed : 15.03 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.12), residues: 4666 helix: 2.00 (0.09), residues: 2981 sheet: -0.78 (0.98), residues: 35 loop : -0.50 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG n 30 TYR 0.021 0.002 TYR r 406 PHE 0.029 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS l 534 Details of bonding type rmsd covalent geometry : bond 0.00383 (40726) covalent geometry : angle 0.58341 (54936) SS BOND : bond 0.00462 ( 7) SS BOND : angle 1.77483 ( 14) hydrogen bonds : bond 0.05483 ( 2336) hydrogen bonds : angle 4.23761 ( 6786) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 700 time to evaluate : 1.563 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8391 (mmt) cc_final: 0.8007 (mmt) REVERT: S 48 MET cc_start: 0.9185 (mtp) cc_final: 0.8899 (mtm) REVERT: V 8 LYS cc_start: 0.8351 (mttt) cc_final: 0.8085 (mtmm) REVERT: V 106 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7308 (mtt90) REVERT: Y 99 ILE cc_start: 0.7505 (mt) cc_final: 0.7035 (tt) REVERT: Z 49 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7874 (mm-30) REVERT: a 114 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9025 (ptmm) REVERT: a 152 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8900 (ttmm) REVERT: b 9 LYS cc_start: 0.8372 (mtpt) cc_final: 0.8130 (mtpp) REVERT: b 93 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8105 (mttt) REVERT: b 119 LEU cc_start: 0.8806 (mm) cc_final: 0.8601 (mm) REVERT: e 111 ASP cc_start: 0.7838 (t70) cc_final: 0.7269 (t0) REVERT: e 115 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: f 61 GLN cc_start: 0.8882 (tp40) cc_final: 0.8515 (tp-100) REVERT: f 65 ASP cc_start: 0.8774 (m-30) cc_final: 0.8473 (m-30) REVERT: g 16 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8712 (mt) REVERT: h 5 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8270 (t70) REVERT: h 13 ASP cc_start: 0.8563 (t0) cc_final: 0.7915 (t0) REVERT: h 102 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: j 85 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8392 (mttt) REVERT: m 99 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7525 (ttm) REVERT: m 135 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8322 (t80) REVERT: n 54 GLU cc_start: 0.7812 (pm20) cc_final: 0.7441 (mp0) REVERT: o 111 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8211 (ttpp) REVERT: p 70 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: s 206 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8419 (mp0) REVERT: s 227 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8254 (tp30) REVERT: s 296 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8921 (tt) REVERT: u 37 ASP cc_start: 0.8663 (t70) cc_final: 0.8330 (t0) REVERT: v 48 ASP cc_start: 0.8462 (m-30) cc_final: 0.8235 (m-30) REVERT: v 97 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8486 (mtpt) REVERT: w 45 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8104 (pp) REVERT: w 272 ASP cc_start: 0.8143 (m-30) cc_final: 0.7727 (m-30) REVERT: w 293 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7930 (ttp80) outliers start: 129 outliers final: 61 residues processed: 765 average time/residue: 0.7924 time to fit residues: 723.8155 Evaluate side-chains 749 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 673 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 190 MET Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 492 ILE Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 185 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 393 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 268 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 397 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN U 62 ASN W 90 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN b 13 GLN d 149 HIS i 47 ASN i 171 ASN k 50 ASN ** l 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 ASN r 251 ASN r 304 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.085885 restraints weight = 52720.129| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.29 r_work: 0.2740 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40734 Z= 0.172 Angle : 0.596 10.249 54950 Z= 0.300 Chirality : 0.042 0.194 5931 Planarity : 0.005 0.065 6684 Dihedral : 16.272 179.072 6681 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 3.32 % Allowed : 15.30 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.12), residues: 4666 helix: 2.01 (0.09), residues: 2984 sheet: -0.67 (0.98), residues: 35 loop : -0.50 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 30 TYR 0.022 0.002 TYR r 406 PHE 0.028 0.002 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS S 27 Details of bonding type rmsd covalent geometry : bond 0.00409 (40726) covalent geometry : angle 0.59554 (54936) SS BOND : bond 0.00521 ( 7) SS BOND : angle 1.79316 ( 14) hydrogen bonds : bond 0.05536 ( 2336) hydrogen bonds : angle 4.22252 ( 6786) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 683 time to evaluate : 1.585 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8375 (mmt) cc_final: 0.7970 (mmt) REVERT: S 48 MET cc_start: 0.9192 (mtp) cc_final: 0.8907 (mtm) REVERT: V 8 LYS cc_start: 0.8326 (mttt) cc_final: 0.8065 (mtmm) REVERT: V 106 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7279 (mtt90) REVERT: Y 99 ILE cc_start: 0.7532 (mt) cc_final: 0.7012 (tt) REVERT: Z 49 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: a 103 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: a 114 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9057 (ptmm) REVERT: a 152 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8898 (ttmm) REVERT: b 9 LYS cc_start: 0.8374 (mtpt) cc_final: 0.8129 (mtpt) REVERT: b 93 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8131 (mttt) REVERT: b 119 LEU cc_start: 0.8811 (mm) cc_final: 0.8606 (mm) REVERT: e 111 ASP cc_start: 0.7877 (t70) cc_final: 0.7248 (t0) REVERT: e 115 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: f 61 GLN cc_start: 0.8932 (tp40) cc_final: 0.8533 (tp-100) REVERT: f 65 ASP cc_start: 0.8775 (m-30) cc_final: 0.8536 (m-30) REVERT: h 5 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8303 (t70) REVERT: h 13 ASP cc_start: 0.8578 (t0) cc_final: 0.7923 (t0) REVERT: h 102 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: j 85 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8404 (mttt) REVERT: l 411 MET cc_start: 0.8914 (mmp) cc_final: 0.8710 (mmp) REVERT: m 99 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7504 (ttm) REVERT: m 135 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8258 (t80) REVERT: n 41 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8873 (mttm) REVERT: n 54 GLU cc_start: 0.7850 (pm20) cc_final: 0.7493 (mp0) REVERT: p 70 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: r 375 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9031 (tp) REVERT: s 206 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8442 (mp0) REVERT: s 227 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8281 (tp30) REVERT: s 296 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8943 (tt) REVERT: u 37 ASP cc_start: 0.8669 (t70) cc_final: 0.8302 (t0) REVERT: u 155 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7676 (pp20) REVERT: u 172 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8545 (mtp) REVERT: v 97 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8458 (mtpt) REVERT: v 118 ARG cc_start: 0.6799 (tmm-80) cc_final: 0.6507 (ttp80) REVERT: w 293 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7891 (ttp80) outliers start: 137 outliers final: 76 residues processed: 749 average time/residue: 0.7888 time to fit residues: 705.0134 Evaluate side-chains 758 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 664 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain a residue 189 ASN Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 190 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 492 ILE Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain u residue 172 MET Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 304 optimal weight: 4.9990 chunk 348 optimal weight: 4.9990 chunk 393 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 451 optimal weight: 2.9990 chunk 52 optimal weight: 0.0070 chunk 289 optimal weight: 0.8980 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN U 62 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN b 13 GLN i 47 ASN i 171 ASN k 50 ASN ** l 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 ASN r 304 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.087550 restraints weight = 52562.944| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.25 r_work: 0.2777 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40734 Z= 0.134 Angle : 0.567 9.719 54950 Z= 0.286 Chirality : 0.041 0.182 5931 Planarity : 0.005 0.064 6684 Dihedral : 15.751 179.598 6679 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 3.10 % Allowed : 15.54 % Favored : 81.36 % 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: 1.86 (0.12), residues: 4666 helix: 2.16 (0.09), residues: 2979 sheet: -0.56 (0.98), residues: 35 loop : -0.46 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 30 TYR 0.022 0.001 TYR r 406 PHE 0.028 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00301 (40726) covalent geometry : angle 0.56648 (54936) SS BOND : bond 0.00416 ( 7) SS BOND : angle 1.66218 ( 14) hydrogen bonds : bond 0.05001 ( 2336) hydrogen bonds : angle 4.13730 ( 6786) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 692 time to evaluate : 1.484 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8369 (mmt) cc_final: 0.7997 (mmt) REVERT: S 48 MET cc_start: 0.9180 (mtp) cc_final: 0.8927 (mtm) REVERT: V 8 LYS cc_start: 0.8315 (mttt) cc_final: 0.8052 (mtmm) REVERT: V 106 ARG cc_start: 0.8019 (mtt90) cc_final: 0.7204 (mtt90) REVERT: Y 99 ILE cc_start: 0.7459 (mt) cc_final: 0.6976 (tt) REVERT: Z 39 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7613 (mtp85) REVERT: Z 49 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: a 103 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: a 114 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9035 (ptmm) REVERT: a 152 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8892 (ttmm) REVERT: b 9 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8074 (mtpt) REVERT: c 149 ILE cc_start: 0.8699 (pp) cc_final: 0.8491 (pt) REVERT: c 165 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8287 (t70) REVERT: e 115 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: f 61 GLN cc_start: 0.8948 (tp40) cc_final: 0.8556 (tp-100) REVERT: h 5 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8296 (t70) REVERT: h 13 ASP cc_start: 0.8515 (t0) cc_final: 0.7863 (t0) REVERT: h 102 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: j 85 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8379 (mttt) REVERT: l 411 MET cc_start: 0.8864 (mmp) cc_final: 0.8620 (mmp) REVERT: m 99 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7502 (ttm) REVERT: m 135 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8171 (t80) REVERT: n 41 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8864 (mttm) REVERT: n 54 GLU cc_start: 0.7882 (pm20) cc_final: 0.7513 (mp0) REVERT: o 111 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8054 (mttt) REVERT: p 70 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: s 206 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8413 (mp0) REVERT: s 227 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8231 (tp30) REVERT: s 296 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8891 (tt) REVERT: u 37 ASP cc_start: 0.8676 (t70) cc_final: 0.8304 (t0) REVERT: u 155 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7578 (pp20) REVERT: u 172 MET cc_start: 0.9076 (mtp) cc_final: 0.8489 (mtp) REVERT: v 39 MET cc_start: 0.8303 (tpt) cc_final: 0.7891 (tpp) REVERT: v 97 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8407 (mtpt) REVERT: v 118 ARG cc_start: 0.6822 (tmm-80) cc_final: 0.6506 (ttp80) REVERT: w 238 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: w 272 ASP cc_start: 0.8145 (m-30) cc_final: 0.7748 (m-30) outliers start: 128 outliers final: 64 residues processed: 763 average time/residue: 0.7877 time to fit residues: 716.2142 Evaluate side-chains 754 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 672 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 310 MET Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain v residue 35 LYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 238 GLU Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 259 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 388 optimal weight: 3.9990 chunk 374 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 357 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN U 62 ASN W 90 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN i 47 ASN i 171 ASN k 50 ASN o 126 ASN r 304 GLN r 415 GLN u 77 HIS v 54 GLN w 107 GLN 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 = 0.106562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.086553 restraints weight = 52504.353| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.29 r_work: 0.2754 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40734 Z= 0.159 Angle : 0.590 13.307 54950 Z= 0.296 Chirality : 0.042 0.189 5931 Planarity : 0.005 0.062 6684 Dihedral : 15.548 179.387 6679 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 2.93 % Allowed : 16.15 % Favored : 80.92 % 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 (0.12), residues: 4666 helix: 2.12 (0.09), residues: 2981 sheet: -0.52 (0.98), residues: 35 loop : -0.47 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 30 TYR 0.022 0.001 TYR r 406 PHE 0.029 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00373 (40726) covalent geometry : angle 0.58982 (54936) SS BOND : bond 0.00497 ( 7) SS BOND : angle 1.73879 ( 14) hydrogen bonds : bond 0.05256 ( 2336) hydrogen bonds : angle 4.16175 ( 6786) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 672 time to evaluate : 1.494 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8384 (mmt) cc_final: 0.8003 (mmt) REVERT: S 48 MET cc_start: 0.9191 (mtp) cc_final: 0.8938 (mtm) REVERT: V 8 LYS cc_start: 0.8310 (mttt) cc_final: 0.8038 (mtmm) REVERT: V 106 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7236 (mtt90) REVERT: Y 99 ILE cc_start: 0.7462 (mt) cc_final: 0.6953 (tt) REVERT: Z 39 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7598 (mtp85) REVERT: Z 49 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: a 103 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: a 114 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.9048 (ptmm) REVERT: a 130 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: a 152 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8904 (ttmm) REVERT: b 9 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8133 (mtpt) REVERT: b 93 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8126 (mttt) REVERT: c 149 ILE cc_start: 0.8768 (pp) cc_final: 0.8528 (pt) REVERT: e 111 ASP cc_start: 0.7783 (t70) cc_final: 0.7248 (t0) REVERT: e 115 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: f 61 GLN cc_start: 0.8898 (tp40) cc_final: 0.8524 (tp-100) REVERT: f 65 ASP cc_start: 0.8890 (m-30) cc_final: 0.8550 (m-30) REVERT: h 5 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8280 (t70) REVERT: h 13 ASP cc_start: 0.8539 (t0) cc_final: 0.7981 (t0) REVERT: h 102 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7757 (pt0) REVERT: j 85 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8377 (mttt) REVERT: l 411 MET cc_start: 0.8854 (mmp) cc_final: 0.8653 (mmp) REVERT: m 99 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7494 (ttm) REVERT: m 135 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8203 (t80) REVERT: n 41 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8857 (mttm) REVERT: n 54 GLU cc_start: 0.7883 (pm20) cc_final: 0.7516 (mp0) REVERT: p 44 MET cc_start: 0.8923 (tpp) cc_final: 0.8575 (tpp) REVERT: p 70 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: r 304 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8096 (pt0) REVERT: r 375 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8981 (tp) REVERT: s 206 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8409 (mp0) REVERT: s 227 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: s 274 ARG cc_start: 0.9282 (ttt180) cc_final: 0.8966 (ttt180) REVERT: s 296 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8922 (tt) REVERT: u 37 ASP cc_start: 0.8666 (t70) cc_final: 0.8283 (t0) REVERT: u 155 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: u 172 MET cc_start: 0.9028 (mtp) cc_final: 0.8421 (mtp) REVERT: v 97 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8420 (mtpt) REVERT: w 272 ASP cc_start: 0.8142 (m-30) cc_final: 0.7728 (m-30) outliers start: 121 outliers final: 74 residues processed: 737 average time/residue: 0.8089 time to fit residues: 708.5362 Evaluate side-chains 756 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 662 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain r residue 310 MET Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain v residue 35 LYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 109 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 452 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN U 62 ASN U 71 GLN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN i 47 ASN i 171 ASN k 50 ASN o 126 ASN r 304 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.085846 restraints weight = 52675.245| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.29 r_work: 0.2739 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 40734 Z= 0.186 Angle : 0.618 12.841 54950 Z= 0.310 Chirality : 0.043 0.200 5931 Planarity : 0.005 0.062 6684 Dihedral : 15.459 179.182 6679 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 2.84 % Allowed : 16.44 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.12), residues: 4666 helix: 2.04 (0.09), residues: 2987 sheet: -0.50 (0.99), residues: 35 loop : -0.49 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG n 30 TYR 0.021 0.002 TYR r 406 PHE 0.029 0.002 PHE i 292 TRP 0.022 0.001 TRP u 86 HIS 0.007 0.001 HIS S 27 Details of bonding type rmsd covalent geometry : bond 0.00445 (40726) covalent geometry : angle 0.61704 (54936) SS BOND : bond 0.00570 ( 7) SS BOND : angle 1.82315 ( 14) hydrogen bonds : bond 0.05595 ( 2336) hydrogen bonds : angle 4.21178 ( 6786) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 673 time to evaluate : 1.598 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8403 (mmt) cc_final: 0.8013 (mmt) REVERT: S 48 MET cc_start: 0.9196 (mtp) cc_final: 0.8905 (mtm) REVERT: V 8 LYS cc_start: 0.8334 (mttt) cc_final: 0.8078 (mtmm) REVERT: V 26 THR cc_start: 0.9333 (t) cc_final: 0.9113 (m) REVERT: V 106 ARG cc_start: 0.8036 (mtt90) cc_final: 0.7253 (mtt90) REVERT: X 105 MET cc_start: 0.8400 (mmm) cc_final: 0.8182 (mmm) REVERT: Y 99 ILE cc_start: 0.7474 (mt) cc_final: 0.6961 (tt) REVERT: Z 39 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7603 (mtp85) REVERT: Z 49 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: Z 86 TYR cc_start: 0.5844 (OUTLIER) cc_final: 0.5429 (t80) REVERT: a 114 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9054 (ptmm) REVERT: a 130 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: a 152 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8904 (ttmm) REVERT: b 9 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8149 (mtpt) REVERT: e 111 ASP cc_start: 0.7993 (t70) cc_final: 0.7404 (t0) REVERT: f 61 GLN cc_start: 0.8907 (tp40) cc_final: 0.8551 (tp-100) REVERT: f 65 ASP cc_start: 0.8837 (m-30) cc_final: 0.8527 (m-30) REVERT: h 5 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8311 (t70) REVERT: h 13 ASP cc_start: 0.8550 (t0) cc_final: 0.8003 (t0) REVERT: h 102 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: j 85 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8386 (mttt) REVERT: l 411 MET cc_start: 0.8870 (mmp) cc_final: 0.8608 (mmp) REVERT: m 99 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7510 (ttm) REVERT: m 135 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8236 (t80) REVERT: n 41 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8867 (mttm) REVERT: n 54 GLU cc_start: 0.7891 (pm20) cc_final: 0.7519 (mp0) REVERT: p 44 MET cc_start: 0.8944 (tpp) cc_final: 0.8631 (tpp) REVERT: p 70 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: p 138 LYS cc_start: 0.8351 (tptt) cc_final: 0.8079 (ttpp) REVERT: r 375 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8997 (tp) REVERT: s 206 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8439 (mp0) REVERT: s 227 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8288 (tp30) REVERT: s 277 TYR cc_start: 0.8723 (m-80) cc_final: 0.8323 (m-10) REVERT: s 296 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8945 (tt) REVERT: u 37 ASP cc_start: 0.8679 (t70) cc_final: 0.8288 (t0) REVERT: u 155 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7653 (pp20) REVERT: u 172 MET cc_start: 0.8995 (mtp) cc_final: 0.8457 (mtp) REVERT: w 45 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8113 (pp) outliers start: 117 outliers final: 75 residues processed: 734 average time/residue: 0.8296 time to fit residues: 725.9262 Evaluate side-chains 755 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 662 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 68 ASP Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 134 GLN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 170 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 310 MET Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain v residue 35 LYS Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 342 optimal weight: 0.6980 chunk 389 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 381 optimal weight: 0.6980 chunk 351 optimal weight: 4.9990 chunk 189 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 100 optimal weight: 0.0000 chunk 343 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN U 62 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN i 47 ASN i 171 ASN k 50 ASN l 59 GLN o 126 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN w 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.110475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.091055 restraints weight = 52314.118| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.25 r_work: 0.2826 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 40734 Z= 0.114 Angle : 0.553 11.518 54950 Z= 0.277 Chirality : 0.039 0.185 5931 Planarity : 0.004 0.062 6684 Dihedral : 14.621 174.825 6679 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 1.72 % Allowed : 17.65 % Favored : 80.63 % 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: 2.31 (0.09), residues: 2978 sheet: -0.34 (0.99), residues: 35 loop : -0.38 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG v 118 TYR 0.026 0.001 TYR r 406 PHE 0.031 0.001 PHE i 292 TRP 0.024 0.001 TRP l 144 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00244 (40726) covalent geometry : angle 0.55202 (54936) SS BOND : bond 0.00295 ( 7) SS BOND : angle 1.54034 ( 14) hydrogen bonds : bond 0.04331 ( 2336) hydrogen bonds : angle 4.03751 ( 6786) Misc. bond : bond 0.00026 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 711 time to evaluate : 0.915 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8363 (mmt) cc_final: 0.8034 (mmt) REVERT: S 48 MET cc_start: 0.9145 (mtp) cc_final: 0.8876 (mtm) REVERT: V 8 LYS cc_start: 0.8309 (mttt) cc_final: 0.8052 (mtmm) REVERT: V 106 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7283 (mtt90) REVERT: Y 99 ILE cc_start: 0.7385 (mt) cc_final: 0.6920 (tt) REVERT: Z 39 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7391 (mtp85) REVERT: Z 49 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: Z 86 TYR cc_start: 0.5999 (OUTLIER) cc_final: 0.5445 (t80) REVERT: a 114 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.9025 (ptmm) REVERT: b 9 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8077 (mtpt) REVERT: b 85 TYR cc_start: 0.9150 (t80) cc_final: 0.8910 (t80) REVERT: c 165 ASP cc_start: 0.8590 (t70) cc_final: 0.8181 (t70) REVERT: e 111 ASP cc_start: 0.7916 (t70) cc_final: 0.7378 (t0) REVERT: f 61 GLN cc_start: 0.8898 (tp40) cc_final: 0.8434 (tp-100) REVERT: f 65 ASP cc_start: 0.8762 (m-30) cc_final: 0.8361 (m-30) REVERT: h 5 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8280 (t70) REVERT: h 13 ASP cc_start: 0.8349 (t0) cc_final: 0.7750 (t0) REVERT: h 102 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: j 85 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8314 (mttt) REVERT: k 21 MET cc_start: 0.8041 (mtt) cc_final: 0.7617 (mtt) REVERT: l 496 MET cc_start: 0.8565 (mmp) cc_final: 0.8336 (mmm) REVERT: m 99 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7465 (ttm) REVERT: n 41 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8799 (mttm) REVERT: n 54 GLU cc_start: 0.7845 (pm20) cc_final: 0.7537 (mp0) REVERT: o 111 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8325 (ttpp) REVERT: p 159 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7495 (mtpt) REVERT: r 398 MET cc_start: 0.8273 (mmm) cc_final: 0.7585 (ttm) REVERT: s 206 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8380 (mp0) REVERT: s 227 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8325 (tp30) REVERT: s 296 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8856 (tt) REVERT: u 37 ASP cc_start: 0.8626 (t70) cc_final: 0.8264 (t0) REVERT: u 155 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: u 172 MET cc_start: 0.8889 (mtp) cc_final: 0.8336 (mtp) REVERT: v 39 MET cc_start: 0.8214 (tpt) cc_final: 0.7844 (tpp) REVERT: v 48 ASP cc_start: 0.8373 (m-30) cc_final: 0.8137 (m-30) REVERT: w 272 ASP cc_start: 0.8072 (m-30) cc_final: 0.7687 (m-30) outliers start: 71 outliers final: 31 residues processed: 746 average time/residue: 0.7864 time to fit residues: 698.3888 Evaluate side-chains 724 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 680 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain p residue 159 LYS Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain v residue 35 LYS Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 208 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 370 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 155 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 131 optimal weight: 0.0010 chunk 11 optimal weight: 4.9990 chunk 282 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 36 GLN U 40 ASN W 90 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN i 47 ASN i 171 ASN k 50 ASN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.091185 restraints weight = 52614.444| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.25 r_work: 0.2830 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 40734 Z= 0.113 Angle : 0.550 11.202 54950 Z= 0.275 Chirality : 0.039 0.197 5931 Planarity : 0.004 0.060 6684 Dihedral : 14.123 170.457 6678 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 1.38 % Allowed : 18.30 % Favored : 80.32 % 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: 2.13 (0.13), residues: 4666 helix: 2.36 (0.09), residues: 2977 sheet: -0.30 (0.98), residues: 35 loop : -0.31 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG v 118 TYR 0.024 0.001 TYR r 406 PHE 0.031 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.005 0.001 HIS u 77 Details of bonding type rmsd covalent geometry : bond 0.00245 (40726) covalent geometry : angle 0.55003 (54936) SS BOND : bond 0.00337 ( 7) SS BOND : angle 1.51327 ( 14) hydrogen bonds : bond 0.04287 ( 2336) hydrogen bonds : angle 3.99888 ( 6786) Misc. bond : bond 0.00019 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16256.72 seconds wall clock time: 276 minutes 39.75 seconds (16599.75 seconds total)