Starting phenix.real_space_refine on Mon Jul 6 23:07:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vy9_32197/07_2026/7vy9_32197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vy9_32197/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vy9_32197/07_2026/7vy9_32197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vy9_32197/07_2026/7vy9_32197.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vy9_32197/07_2026/7vy9_32197.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vy9_32197/07_2026/7vy9_32197.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vy9_32197/07_2026/7vy9_32197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vy9_32197/07_2026/7vy9_32197.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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-6108/lib/python3.11/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: 7.87, per 1000 atoms: 0.20 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: 2.91 Conformation dependent library (CDL) restraints added in 1.7 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: 1.07 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: 7.29 Time building geometry restraints manager: 3.95 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: 23444 35.69 - 71.38: 1101 71.38 - 107.07: 63 107.07 - 142.76: 11 142.76 - 178.45: 17 Dihedral angle restraints: 24636 sinusoidal: 10776 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 24633 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: 2.030 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.060 Process input model: 32.500 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 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 : 19.097 178.447 15661 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/Z covalent geometry : bond 0.00785 / 0.43 (40726) covalent geometry : angle 0.86261 / 0.42 (54936) SS BOND : bond 0.00208 / 0.11 ( 7) SS BOND : angle 1.48578 / 0.92 ( 14) hydrogen bonds : bond 0.13222 / 8.68 ( 2336) hydrogen bonds : angle 5.49009 / 4.02 ( 6786) Misc. bond : bond 0.21830 / 11.49 ( 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 : 1.481 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: 0.7354 time to fit residues: 630.6152 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 : 1.384 ------------------------------------------------------------------------------- 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... 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 = 0.3191 r_free = 0.3191 target = 0.108572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.088745 restraints weight = 52541.118| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.25 r_work: 0.2783 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 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 = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0741 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= 0.163 Angle : 0.587 9.548 54950 Z= 0.296 Chirality : 0.042 0.191 5931 Planarity : 0.005 0.067 6684 Dihedral : 16.804 179.989 6436 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 2.74 % Allowed : 13.21 % Favored : 84.05 % 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: -0.72 (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/Z covalent geometry : bond 0.00381 / 0.16 (40726) covalent geometry : angle 0.58668 / 0.30 (54936) SS BOND : bond 0.00278 / 0.14 ( 7) SS BOND : angle 1.52997 / 0.81 ( 14) hydrogen bonds : bond 0.05449 / 3.68 ( 2336) hydrogen bonds : angle 4.33180 / 3.16 ( 6786) Misc. bond : bond 0.00162 / 0.09 ( 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 810 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 697 time to evaluate : 1.441 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: 0.9144 (mtp) cc_final: 0.8841 (mtm) REVERT: U 79 GLU cc_start: 0.7948 (tp30) cc_final: 0.7671 (mm-30) REVERT: Y 91 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7986 (tm-30) REVERT: Z 30 GLU cc_start: 0.8325 (tt0) cc_final: 0.8061 (mt-10) REVERT: Z 49 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: a 76 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8855 (mp) REVERT: b 9 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8129 (mtpp) REVERT: b 93 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8073 (mttt) REVERT: c 74 ASP cc_start: 0.7971 (t0) cc_final: 0.7693 (t0) REVERT: c 149 ILE cc_start: 0.8732 (pp) cc_final: 0.8499 (pt) REVERT: h 5 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8288 (t0) REVERT: h 13 ASP cc_start: 0.8459 (t0) cc_final: 0.7934 (t0) REVERT: i 245 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8791 (tmm) REVERT: l 383 MET cc_start: 0.8913 (tpp) cc_final: 0.8623 (tpt) REVERT: m 99 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7529 (ttm) REVERT: o 61 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: o 111 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8069 (mttt) REVERT: s 227 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8363 (tp30) REVERT: u 37 ASP cc_start: 0.8503 (t0) cc_final: 0.8287 (t0) REVERT: u 155 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8029 (pp20) REVERT: w 241 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.7374 (t80) outliers start: 113 outliers final: 37 residues processed: 744 average time/residue: 0.7356 time to fit residues: 655.5993 Evaluate side-chains 723 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 676 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 18 ASP 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 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 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: 2.9990 chunk 84 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 222 optimal weight: 0.6980 chunk 403 optimal weight: 5.9990 chunk 357 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 408 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN U 62 ASN W 90 ASN Z 60 ASN b 13 GLN b 89 HIS h 70 GLN i 47 ASN i 171 ASN k 50 ASN l 446 ASN l 580 GLN o 126 ASN r 43 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 = 0.3176 r_free = 0.3176 target = 0.107497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.087687 restraints weight = 52650.758| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.25 r_work: 0.2775 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- 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 = 0.77 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 = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 40734 Z= 0.159 Angle : 0.572 9.813 54950 Z= 0.289 Chirality : 0.042 0.189 5931 Planarity : 0.005 0.062 6684 Dihedral : 15.838 176.194 6410 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.44 % Rotamer: Outliers : 3.30 % Allowed : 13.48 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.12), residues: 4666 helix: 2.12 (0.09), residues: 2989 sheet: -0.56 (1.16), residues: 25 loop : -0.39 (0.16), residues: 1652 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 0.021 0.001 TRP u 86 HIS 0.008 0.001 HIS S 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (40726) covalent geometry : angle 0.57143 / 0.29 (54936) SS BOND : bond 0.00599 / 0.40 ( 7) SS BOND : angle 1.66467 / 0.98 ( 14) hydrogen bonds : bond 0.05364 / 3.63 ( 2336) hydrogen bonds : angle 4.22727 / 3.08 ( 6786) Misc. bond : bond 0.00104 / 0.05 ( 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 832 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 696 time to evaluate : 1.552 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: 0.9170 (mtp) cc_final: 0.8877 (mtm) REVERT: Z 30 GLU cc_start: 0.8446 (tt0) cc_final: 0.8216 (mt-10) REVERT: Z 49 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: a 114 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8981 (ptmm) REVERT: b 9 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8101 (mtpp) REVERT: b 93 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8078 (mttt) REVERT: c 60 GLU cc_start: 0.8918 (mp0) cc_final: 0.8606 (mp0) REVERT: e 111 ASP cc_start: 0.7799 (t70) cc_final: 0.7211 (t0) REVERT: e 115 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7564 (mt0) REVERT: e 127 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8648 (ttpt) REVERT: f 61 GLN cc_start: 0.8888 (tp40) cc_final: 0.8493 (tp-100) REVERT: h 13 ASP cc_start: 0.8457 (t0) cc_final: 0.7864 (t0) REVERT: h 102 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: j 85 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8384 (mttt) REVERT: m 77 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: m 99 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7500 (ttm) REVERT: m 135 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8359 (t80) REVERT: r 355 MET cc_start: 0.9200 (tpp) cc_final: 0.8993 (mmp) REVERT: s 206 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8322 (mp0) REVERT: s 227 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: s 296 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8930 (tt) REVERT: u 37 ASP cc_start: 0.8551 (t70) cc_final: 0.8272 (t0) REVERT: u 155 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8001 (pp20) REVERT: v 48 ASP cc_start: 0.8389 (m-30) cc_final: 0.8158 (m-30) REVERT: w 241 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.7196 (t80) outliers start: 136 outliers final: 64 residues processed: 751 average time/residue: 0.7332 time to fit residues: 658.7401 Evaluate side-chains 746 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 668 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 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 138 GLU Chi-restraints excluded: chain V residue 141 VAL 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 Z residue 82 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 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 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 72 ASP Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 127 LYS Chi-restraints excluded: chain f residue 58 LEU 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 100 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 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 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 42 SER Chi-restraints excluded: chain n residue 46 LYS 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 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 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: 4.9990 chunk 435 optimal weight: 0.9990 chunk 372 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 370 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN Z 60 ASN h 45 HIS h 70 GLN i 47 ASN i 171 ASN k 50 ASN l 170 GLN l 534 HIS ** l 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 ASN r 103 GLN s 230 ASN u 77 HIS v 54 GLN v 117 GLN w 107 GLN w 235 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.086863 restraints weight = 52519.876| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.25 r_work: 0.2754 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40734 Z= 0.186 Angle : 0.593 9.932 54950 Z= 0.300 Chirality : 0.043 0.197 5931 Planarity : 0.005 0.062 6684 Dihedral : 15.422 172.522 6407 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 3.54 % Allowed : 14.01 % Favored : 82.45 % 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: 1.77 (0.12), residues: 4666 helix: 2.06 (0.09), residues: 2982 sheet: -0.48 (1.16), residues: 25 loop : -0.42 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 0.008 0.001 HIS S 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (40726) covalent geometry : angle 0.59224 / 0.30 (54936) SS BOND : bond 0.00496 / 0.32 ( 7) SS BOND : angle 1.88272 / 1.15 ( 14) hydrogen bonds : bond 0.05615 / 3.80 ( 2336) hydrogen bonds : angle 4.23400 / 3.08 ( 6786) Misc. bond : bond 0.00002 / 0.00 ( 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 830 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 684 time to evaluate : 1.649 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: Q 52 MET cc_start: 0.8386 (mmt) cc_final: 0.8036 (mmt) REVERT: S 48 MET cc_start: 0.9184 (mtp) cc_final: 0.8898 (mtm) REVERT: V 8 LYS cc_start: 0.8348 (mttt) cc_final: 0.8085 (mtmm) REVERT: Y 99 ILE cc_start: 0.7479 (mt) cc_final: 0.7011 (tt) REVERT: Z 30 GLU cc_start: 0.8455 (tt0) cc_final: 0.8208 (mt-10) REVERT: Z 49 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: a 103 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: a 114 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9052 (ptmm) REVERT: a 152 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8926 (ttmm) REVERT: b 9 LYS cc_start: 0.8393 (mtpt) cc_final: 0.8119 (mtpp) REVERT: b 93 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8103 (mttt) REVERT: b 119 LEU cc_start: 0.8727 (mm) cc_final: 0.8476 (mp) REVERT: e 111 ASP cc_start: 0.7864 (t70) cc_final: 0.7217 (t0) REVERT: e 115 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7608 (mt0) REVERT: e 116 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: e 127 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8664 (ttpt) REVERT: f 61 GLN cc_start: 0.8893 (tp40) cc_final: 0.8531 (tp-100) REVERT: h 5 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8349 (t70) REVERT: h 13 ASP cc_start: 0.8493 (t0) cc_final: 0.7881 (t0) REVERT: h 102 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7576 (pt0) REVERT: j 85 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8392 (mttt) REVERT: m 77 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: m 99 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7515 (ttm) REVERT: m 135 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8354 (t80) REVERT: n 41 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8897 (mttm) REVERT: n 54 GLU cc_start: 0.7782 (pm20) cc_final: 0.7379 (mp0) REVERT: o 111 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8089 (mttt) REVERT: p 44 MET cc_start: 0.8914 (mmt) cc_final: 0.8548 (tpp) REVERT: s 206 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8409 (mp0) REVERT: s 227 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: s 296 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8973 (tt) REVERT: u 37 ASP cc_start: 0.8646 (t70) cc_final: 0.8307 (t0) REVERT: v 48 ASP cc_start: 0.8443 (m-30) cc_final: 0.8171 (m-30) REVERT: w 272 ASP cc_start: 0.8202 (m-30) cc_final: 0.7733 (m-30) outliers start: 146 outliers final: 77 residues processed: 747 average time/residue: 0.7359 time to fit residues: 657.3698 Evaluate side-chains 759 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 665 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 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 138 GLU Chi-restraints excluded: chain V residue 141 VAL 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 Z residue 82 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 76 LEU 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 152 LYS 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 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 e residue 116 GLU Chi-restraints excluded: chain e residue 127 LYS Chi-restraints excluded: chain f residue 58 LEU 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 18 MET 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 100 MET Chi-restraints excluded: chain i residue 164 ILE 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 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 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 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 m residue 170 GLU Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 46 LYS 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 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 170 THR 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 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 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: 6.9990 chunk 29 optimal weight: 9.9990 chunk 374 optimal weight: 4.9990 chunk 246 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 430 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 h 70 GLN i 47 ASN i 171 ASN i 186 HIS k 50 ASN ** l 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 ASN r 103 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.086053 restraints weight = 52403.723| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.24 r_work: 0.2743 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 40734 Z= 0.197 Angle : 0.610 11.355 54950 Z= 0.308 Chirality : 0.044 0.199 5931 Planarity : 0.005 0.063 6684 Dihedral : 15.061 175.555 6405 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 3.64 % Allowed : 14.50 % Favored : 81.87 % 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: 1.65 (0.12), residues: 4666 helix: 1.98 (0.09), residues: 2988 sheet: -0.84 (0.97), residues: 35 loop : -0.50 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 30 TYR 0.021 0.002 TYR r 406 PHE 0.028 0.002 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.009 0.001 HIS S 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (40726) covalent geometry : angle 0.60928 / 0.31 (54936) SS BOND : bond 0.00610 / 0.41 ( 7) SS BOND : angle 1.91500 / 1.18 ( 14) hydrogen bonds : bond 0.05798 / 3.93 ( 2336) hydrogen bonds : angle 4.25860 / 3.10 ( 6786) Misc. bond : bond 0.00010 / 0.01 ( 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 834 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 684 time to evaluate : 1.035 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: 0.8380 (mmt) cc_final: 0.8020 (mmt) REVERT: S 48 MET cc_start: 0.9186 (mtp) cc_final: 0.8908 (mtm) REVERT: V 8 LYS cc_start: 0.8356 (mttt) cc_final: 0.8071 (mtmm) REVERT: Y 99 ILE cc_start: 0.7501 (mt) cc_final: 0.7002 (tt) REVERT: Z 30 GLU cc_start: 0.8440 (tt0) cc_final: 0.8193 (mt-10) REVERT: Z 49 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: a 103 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: a 114 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9057 (ptmm) REVERT: a 152 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8906 (ttmm) REVERT: b 9 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8145 (mtpp) REVERT: b 93 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8122 (mttt) REVERT: b 119 LEU cc_start: 0.8793 (mm) cc_final: 0.8584 (mm) REVERT: e 111 ASP cc_start: 0.7850 (t70) cc_final: 0.7155 (t0) REVERT: e 115 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7619 (mt0) REVERT: e 116 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: e 127 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8674 (ttpt) REVERT: f 61 GLN cc_start: 0.8887 (tp40) cc_final: 0.8480 (tp-100) REVERT: f 65 ASP cc_start: 0.8746 (m-30) cc_final: 0.8520 (m-30) REVERT: h 5 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8281 (t70) REVERT: h 13 ASP cc_start: 0.8553 (t0) cc_final: 0.7914 (t0) REVERT: h 102 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: j 85 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8418 (mttt) REVERT: l 411 MET cc_start: 0.8939 (mmp) cc_final: 0.8713 (mmp) REVERT: m 77 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: m 99 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7528 (ttm) REVERT: m 135 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8362 (t80) REVERT: n 41 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8897 (mttm) REVERT: n 54 GLU cc_start: 0.7821 (pm20) cc_final: 0.7442 (mp0) REVERT: p 44 MET cc_start: 0.8934 (mmt) cc_final: 0.8661 (tpp) REVERT: p 70 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: s 206 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8410 (mp0) REVERT: s 227 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8253 (tp30) REVERT: s 296 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8987 (tt) REVERT: u 37 ASP cc_start: 0.8662 (t70) cc_final: 0.8321 (t0) REVERT: v 105 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7816 (tp30) REVERT: v 118 ARG cc_start: 0.6832 (tmm-80) cc_final: 0.6478 (ttp80) REVERT: w 45 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8097 (pp) outliers start: 150 outliers final: 76 residues processed: 750 average time/residue: 0.7721 time to fit residues: 692.9318 Evaluate side-chains 766 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 670 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU 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 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 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 Z residue 82 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 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 63 GLU 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 e residue 116 GLU Chi-restraints excluded: chain e residue 127 LYS 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 18 MET 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 100 MET 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 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 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 41 LYS Chi-restraints excluded: chain n residue 46 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 170 THR Chi-restraints excluded: chain r residue 179 ILE 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 126 SER Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain v residue 105 GLU 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: 2.9990 chunk 203 optimal weight: 5.9990 chunk 393 optimal weight: 1.9990 chunk 361 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 268 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 chunk 397 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN U 62 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 o 126 ASN r 304 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 = 0.3174 r_free = 0.3174 target = 0.107462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.087743 restraints weight = 52618.794| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.25 r_work: 0.2767 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40734 Z= 0.139 Angle : 0.564 9.767 54950 Z= 0.285 Chirality : 0.041 0.186 5931 Planarity : 0.005 0.063 6684 Dihedral : 14.490 177.623 6405 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 3.05 % Allowed : 15.37 % Favored : 81.58 % 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: 1.84 (0.12), residues: 4666 helix: 2.14 (0.09), residues: 2982 sheet: -0.58 (0.98), residues: 35 loop : -0.45 (0.16), residues: 1649 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 0.022 0.001 TRP u 86 HIS 0.005 0.001 HIS l 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (40726) covalent geometry : angle 0.56368 / 0.28 (54936) SS BOND : bond 0.00451 / 0.29 ( 7) SS BOND : angle 1.72921 / 1.04 ( 14) hydrogen bonds : bond 0.05120 / 3.47 ( 2336) hydrogen bonds : angle 4.15154 / 3.02 ( 6786) Misc. bond : bond 0.00020 / 0.01 ( 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 818 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 692 time to evaluate : 1.603 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: Q 52 MET cc_start: 0.8423 (mmt) cc_final: 0.8070 (mmt) REVERT: S 48 MET cc_start: 0.9181 (mtp) cc_final: 0.8900 (mtm) REVERT: V 8 LYS cc_start: 0.8313 (mttt) cc_final: 0.8032 (mtmm) REVERT: Y 99 ILE cc_start: 0.7493 (mt) cc_final: 0.7008 (tt) REVERT: Z 30 GLU cc_start: 0.8462 (tt0) cc_final: 0.8218 (mt-10) REVERT: Z 39 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7588 (mtp85) REVERT: Z 49 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: a 114 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8982 (ptmm) REVERT: a 152 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8897 (ttmm) REVERT: b 9 LYS cc_start: 0.8315 (mtpt) cc_final: 0.8052 (mtpp) REVERT: b 93 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8074 (mttt) REVERT: b 119 LEU cc_start: 0.8765 (mm) cc_final: 0.8556 (mm) REVERT: e 111 ASP cc_start: 0.7769 (t70) cc_final: 0.7158 (t0) REVERT: e 115 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: e 116 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: e 127 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8643 (ttpt) REVERT: f 61 GLN cc_start: 0.8920 (tp40) cc_final: 0.8515 (tp-100) REVERT: g 16 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8626 (mt) REVERT: h 5 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8305 (t70) REVERT: h 13 ASP cc_start: 0.8555 (t0) cc_final: 0.7913 (t0) REVERT: h 102 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: j 85 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8392 (mttt) REVERT: l 411 MET cc_start: 0.8875 (mmp) cc_final: 0.8668 (mmp) REVERT: m 99 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7513 (ttm) REVERT: m 135 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8304 (t80) REVERT: n 54 GLU cc_start: 0.7836 (pm20) cc_final: 0.7471 (mp0) REVERT: o 111 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8206 (ttpp) REVERT: p 70 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: s 227 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8257 (tp30) REVERT: s 296 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8900 (tt) REVERT: u 37 ASP cc_start: 0.8659 (t70) cc_final: 0.8300 (t0) outliers start: 126 outliers final: 59 residues processed: 756 average time/residue: 0.8211 time to fit residues: 742.7242 Evaluate side-chains 739 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 663 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU 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 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU 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 39 ARG 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 a residue 114 LYS 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 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 33 THR 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 e residue 116 GLU Chi-restraints excluded: chain e residue 127 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 18 MET 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 164 ILE 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 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 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 492 ILE Chi-restraints excluded: chain l residue 504 LEU 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 m residue 135 PHE 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 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 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: 8.9990 chunk 348 optimal weight: 4.9990 chunk 393 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 303 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 451 optimal weight: 0.9980 chunk 52 optimal weight: 0.0270 chunk 289 optimal weight: 5.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN U 62 ASN W 90 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.088237 restraints weight = 52497.997| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.25 r_work: 0.2780 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 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 = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40734 Z= 0.133 Angle : 0.562 9.514 54950 Z= 0.283 Chirality : 0.041 0.184 5931 Planarity : 0.004 0.063 6684 Dihedral : 14.072 178.878 6405 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 3.01 % Allowed : 15.61 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.12), residues: 4666 helix: 2.20 (0.09), residues: 2983 sheet: -0.49 (0.97), residues: 35 loop : -0.43 (0.16), residues: 1648 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 0.022 0.001 TRP u 86 HIS 0.004 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (40726) covalent geometry : angle 0.56096 / 0.28 (54936) SS BOND : bond 0.00427 / 0.27 ( 7) SS BOND : angle 1.65506 / 0.99 ( 14) hydrogen bonds : bond 0.04931 / 3.34 ( 2336) hydrogen bonds : angle 4.10521 / 2.99 ( 6786) Misc. bond : bond 0.00023 / 0.01 ( 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 807 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 683 time to evaluate : 1.587 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: Q 52 MET cc_start: 0.8403 (mmt) cc_final: 0.8050 (mmt) REVERT: S 48 MET cc_start: 0.9173 (mtp) cc_final: 0.8918 (mtm) REVERT: V 8 LYS cc_start: 0.8323 (mttt) cc_final: 0.8032 (mtmm) REVERT: Y 99 ILE cc_start: 0.7458 (mt) cc_final: 0.6973 (tt) REVERT: Z 30 GLU cc_start: 0.8483 (tt0) cc_final: 0.8226 (tt0) REVERT: Z 39 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7580 (mtp85) REVERT: Z 49 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: a 114 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.9033 (ptmm) REVERT: a 152 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8924 (ttmm) REVERT: b 9 LYS cc_start: 0.8321 (mtpt) cc_final: 0.8052 (mtpp) REVERT: b 93 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8052 (mttt) REVERT: b 119 LEU cc_start: 0.8726 (mm) cc_final: 0.8497 (mm) REVERT: c 149 ILE cc_start: 0.8684 (pp) cc_final: 0.8474 (pt) REVERT: e 115 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: f 61 GLN cc_start: 0.8887 (tp40) cc_final: 0.8500 (tp-100) REVERT: f 65 ASP cc_start: 0.8814 (m-30) cc_final: 0.8510 (m-30) REVERT: h 5 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8286 (t70) REVERT: h 13 ASP cc_start: 0.8501 (t0) cc_final: 0.7866 (t0) REVERT: h 102 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: j 85 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8384 (mttt) REVERT: l 411 MET cc_start: 0.8846 (mmp) cc_final: 0.8571 (mmp) REVERT: m 99 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7498 (ttm) REVERT: m 135 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8163 (t80) REVERT: n 8 VAL cc_start: 0.7262 (OUTLIER) cc_final: 0.6871 (p) REVERT: n 41 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8861 (mttm) REVERT: n 54 GLU cc_start: 0.7891 (pm20) cc_final: 0.7509 (mp0) REVERT: o 111 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8212 (ttpp) REVERT: p 70 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: r 375 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8977 (tp) REVERT: r 448 THR cc_start: 0.8881 (t) cc_final: 0.8626 (p) REVERT: s 227 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: s 274 ARG cc_start: 0.9239 (ttt180) cc_final: 0.8904 (ttt180) REVERT: s 296 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8893 (tt) REVERT: u 37 ASP cc_start: 0.8654 (t70) cc_final: 0.8288 (t0) REVERT: u 155 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: u 172 MET cc_start: 0.9068 (mtp) cc_final: 0.8640 (mtp) REVERT: w 227 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6913 (mtt) REVERT: w 238 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: w 272 ASP cc_start: 0.8199 (m-30) cc_final: 0.7776 (m-30) outliers start: 124 outliers final: 67 residues processed: 749 average time/residue: 0.7919 time to fit residues: 709.7384 Evaluate side-chains 753 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 666 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 U residue 32 LEU 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 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 82 VAL 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 33 THR 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 56 VAL Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 18 MET 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 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 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 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU 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 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 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 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 179 ILE 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 126 SER Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 227 MET 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: 0.8980 chunk 221 optimal weight: 0.2980 chunk 388 optimal weight: 3.9990 chunk 374 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 357 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 40 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 r 415 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.107709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.088065 restraints weight = 52392.931| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.25 r_work: 0.2774 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40734 Z= 0.141 Angle : 0.570 13.186 54950 Z= 0.286 Chirality : 0.041 0.188 5931 Planarity : 0.005 0.062 6684 Dihedral : 13.775 179.995 6405 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 2.96 % Allowed : 15.95 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.12), residues: 4666 helix: 2.19 (0.09), residues: 2979 sheet: -0.49 (0.97), residues: 35 loop : -0.43 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG v 118 TYR 0.022 0.001 TYR r 406 PHE 0.028 0.001 PHE i 292 TRP 0.022 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (40726) covalent geometry : angle 0.56919 / 0.29 (54936) SS BOND : bond 0.00467 / 0.30 ( 7) SS BOND : angle 1.68558 / 1.01 ( 14) hydrogen bonds : bond 0.05000 / 3.39 ( 2336) hydrogen bonds : angle 4.11365 / 2.99 ( 6786) Misc. bond : bond 0.00010 / 0.01 ( 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 809 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 687 time to evaluate : 1.378 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: 0.8405 (mmt) cc_final: 0.8054 (mmt) REVERT: S 48 MET cc_start: 0.9182 (mtp) cc_final: 0.8927 (mtm) REVERT: V 8 LYS cc_start: 0.8315 (mttt) cc_final: 0.8023 (mtmm) REVERT: Y 99 ILE cc_start: 0.7453 (mt) cc_final: 0.6970 (tt) REVERT: Z 30 GLU cc_start: 0.8464 (tt0) cc_final: 0.8226 (mt-10) REVERT: Z 49 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: a 103 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: a 114 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9033 (ptmm) REVERT: a 152 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8907 (ttmm) REVERT: b 9 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8055 (mtpp) REVERT: b 93 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8076 (mttt) REVERT: b 119 LEU cc_start: 0.8708 (mm) cc_final: 0.8503 (mm) REVERT: e 111 ASP cc_start: 0.7771 (t70) cc_final: 0.7100 (t0) REVERT: f 61 GLN cc_start: 0.8903 (tp40) cc_final: 0.8519 (tp-100) REVERT: f 65 ASP cc_start: 0.8832 (m-30) cc_final: 0.8595 (m-30) REVERT: h 5 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8316 (t70) REVERT: h 13 ASP cc_start: 0.8485 (t0) cc_final: 0.7850 (t0) REVERT: h 102 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: j 85 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8392 (mttt) REVERT: l 411 MET cc_start: 0.8849 (mmp) cc_final: 0.8609 (mmp) REVERT: m 99 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7495 (ttm) REVERT: m 135 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8188 (t80) REVERT: n 8 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.6870 (p) REVERT: n 41 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8866 (mttm) REVERT: n 54 GLU cc_start: 0.7885 (pm20) cc_final: 0.7509 (mp0) REVERT: p 70 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: p 159 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7528 (mtpt) REVERT: r 375 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8989 (tp) REVERT: r 448 THR cc_start: 0.8885 (t) cc_final: 0.8625 (p) REVERT: s 227 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: s 296 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8894 (tt) REVERT: u 37 ASP cc_start: 0.8634 (t70) cc_final: 0.8260 (t0) REVERT: u 155 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7750 (pp20) REVERT: u 172 MET cc_start: 0.9081 (mtp) cc_final: 0.8476 (mtp) REVERT: w 272 ASP cc_start: 0.8183 (m-30) cc_final: 0.7748 (m-30) outliers start: 122 outliers final: 69 residues processed: 752 average time/residue: 0.7405 time to fit residues: 667.9665 Evaluate side-chains 755 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 668 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 U residue 32 LEU 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 100 LEU Chi-restraints excluded: chain Z residue 18 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 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 b residue 93 LYS Chi-restraints excluded: chain c residue 33 THR 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 134 GLN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 18 MET 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 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 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 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 492 ILE 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 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 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 p residue 159 LYS Chi-restraints excluded: chain r residue 140 THR 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 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: 4.9990 chunk 149 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 373 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 452 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 l 59 GLN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.089257 restraints weight = 52561.205| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.25 r_work: 0.2794 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- 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 = 0.82 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 = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1397 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= 0.126 Angle : 0.560 11.949 54950 Z= 0.280 Chirality : 0.040 0.183 5931 Planarity : 0.004 0.062 6684 Dihedral : 13.304 177.152 6404 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 2.47 % Allowed : 16.70 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.12), residues: 4666 helix: 2.26 (0.09), residues: 2977 sheet: -0.40 (0.98), residues: 35 loop : -0.39 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG v 118 TYR 0.023 0.001 TYR r 406 PHE 0.029 0.001 PHE i 292 TRP 0.022 0.001 TRP u 86 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (40726) covalent geometry : angle 0.55921 / 0.28 (54936) SS BOND : bond 0.00386 / 0.24 ( 7) SS BOND : angle 1.61041 / 0.96 ( 14) hydrogen bonds : bond 0.04700 / 3.19 ( 2336) hydrogen bonds : angle 4.06597 / 2.96 ( 6786) Misc. bond : bond 0.00014 / 0.01 ( 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 785 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 683 time to evaluate : 1.524 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: 0.8387 (mmt) cc_final: 0.8043 (mmt) REVERT: S 48 MET cc_start: 0.9164 (mtp) cc_final: 0.8903 (mtm) REVERT: V 8 LYS cc_start: 0.8291 (mttt) cc_final: 0.8001 (mtmm) REVERT: Y 99 ILE cc_start: 0.7404 (mt) cc_final: 0.6924 (tt) REVERT: Z 30 GLU cc_start: 0.8459 (tt0) cc_final: 0.8235 (tt0) REVERT: Z 39 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7559 (mtp85) REVERT: Z 49 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: a 114 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8965 (ptmm) REVERT: a 152 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8896 (ttmm) REVERT: b 9 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8063 (mtpt) REVERT: b 93 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8074 (mttt) REVERT: f 61 GLN cc_start: 0.8923 (tp40) cc_final: 0.8508 (tp-100) REVERT: f 65 ASP cc_start: 0.8818 (m-30) cc_final: 0.8577 (m-30) REVERT: h 5 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8278 (t70) REVERT: h 13 ASP cc_start: 0.8450 (t0) cc_final: 0.7845 (t0) REVERT: h 102 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: j 85 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8336 (mttt) REVERT: l 411 MET cc_start: 0.8824 (mmp) cc_final: 0.8587 (mmp) REVERT: l 496 MET cc_start: 0.8573 (mmp) cc_final: 0.8331 (mmm) REVERT: m 99 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7468 (ttm) REVERT: n 41 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8831 (mttm) REVERT: n 54 GLU cc_start: 0.7862 (pm20) cc_final: 0.7527 (mp0) REVERT: o 111 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8313 (ttpp) REVERT: p 44 MET cc_start: 0.8914 (tpp) cc_final: 0.8487 (tpp) REVERT: p 138 LYS cc_start: 0.8351 (tptt) cc_final: 0.8086 (ttpp) REVERT: r 17 MET cc_start: 0.8928 (mmm) cc_final: 0.8672 (mmm) REVERT: r 398 MET cc_start: 0.8413 (mmm) cc_final: 0.7770 (ttm) REVERT: r 448 THR cc_start: 0.8825 (t) cc_final: 0.8555 (p) REVERT: s 227 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8264 (tp30) REVERT: s 296 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8892 (tt) REVERT: u 37 ASP cc_start: 0.8612 (t70) cc_final: 0.8239 (t0) REVERT: u 155 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7744 (pp20) REVERT: u 172 MET cc_start: 0.9034 (mtp) cc_final: 0.8426 (mtp) REVERT: v 122 MET cc_start: 0.6380 (tpt) cc_final: 0.6134 (tpt) REVERT: w 272 ASP cc_start: 0.8152 (m-30) cc_final: 0.7726 (m-30) outliers start: 102 outliers final: 58 residues processed: 732 average time/residue: 0.7325 time to fit residues: 641.1457 Evaluate side-chains 747 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 676 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 U residue 32 LEU 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 18 ASP Chi-restraints excluded: chain Z residue 39 ARG 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 a residue 114 LYS 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 33 THR 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 134 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 100 MET Chi-restraints excluded: chain i residue 164 ILE 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 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 140 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET 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 581 LYS Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain p residue 32 VAL 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 310 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 126 SER Chi-restraints excluded: chain u residue 155 GLU 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: 0.0870 chunk 389 optimal weight: 4.9990 chunk 295 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 381 optimal weight: 0.8980 chunk 351 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 343 optimal weight: 2.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN 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 = 0.3204 r_free = 0.3204 target = 0.109566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.090022 restraints weight = 52359.642| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.25 r_work: 0.2810 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 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 : 0.003 0.048 40734 Z= 0.119 Angle : 0.554 11.765 54950 Z= 0.277 Chirality : 0.040 0.188 5931 Planarity : 0.004 0.061 6684 Dihedral : 12.900 173.257 6404 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.72 % Rotamer: Outliers : 2.16 % Allowed : 17.33 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.12), residues: 4666 helix: 2.32 (0.09), residues: 2978 sheet: -0.39 (0.97), residues: 35 loop : -0.34 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG v 118 TYR 0.023 0.001 TYR r 406 PHE 0.030 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (40726) covalent geometry : angle 0.55400 / 0.28 (54936) SS BOND : bond 0.00368 / 0.23 ( 7) SS BOND : angle 1.55952 / 0.92 ( 14) hydrogen bonds : bond 0.04511 / 3.06 ( 2336) hydrogen bonds : angle 4.02522 / 2.92 ( 6786) Misc. bond : bond 0.00016 / 0.01 ( 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 781 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 692 time to evaluate : 1.551 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: 0.8384 (mmt) cc_final: 0.8032 (mmt) REVERT: S 48 MET cc_start: 0.9152 (mtp) cc_final: 0.8888 (mtm) REVERT: V 8 LYS cc_start: 0.8241 (mttt) cc_final: 0.7934 (mtmm) REVERT: Y 99 ILE cc_start: 0.7377 (mt) cc_final: 0.6908 (tt) REVERT: Z 30 GLU cc_start: 0.8454 (tt0) cc_final: 0.8233 (tt0) REVERT: Z 39 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7332 (mtp85) REVERT: Z 49 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: a 114 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.9004 (ptmm) REVERT: a 152 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8886 (ttmm) REVERT: b 9 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8066 (mtpt) REVERT: b 93 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8080 (mttt) REVERT: b 119 LEU cc_start: 0.8517 (mm) cc_final: 0.8285 (mp) REVERT: f 61 GLN cc_start: 0.8897 (tp40) cc_final: 0.8461 (tp-100) REVERT: f 65 ASP cc_start: 0.8809 (m-30) cc_final: 0.8599 (m-30) REVERT: h 5 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8285 (t70) REVERT: h 13 ASP cc_start: 0.8351 (t0) cc_final: 0.7766 (t0) REVERT: h 102 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: j 85 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8316 (mttt) REVERT: l 411 MET cc_start: 0.8807 (mmp) cc_final: 0.8556 (mmp) REVERT: l 496 MET cc_start: 0.8574 (mmp) cc_final: 0.8338 (mmm) REVERT: m 99 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7465 (ttm) REVERT: n 41 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8846 (mttm) REVERT: n 54 GLU cc_start: 0.7852 (pm20) cc_final: 0.7520 (mp0) REVERT: o 111 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8323 (ttpp) REVERT: p 44 MET cc_start: 0.8893 (tpp) cc_final: 0.8511 (tpp) REVERT: p 159 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7462 (mtpt) REVERT: r 17 MET cc_start: 0.8922 (mmm) cc_final: 0.8668 (mmm) REVERT: r 304 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7970 (pt0) REVERT: r 375 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8925 (tp) REVERT: r 398 MET cc_start: 0.8373 (mmm) cc_final: 0.7722 (ttm) REVERT: s 1 MET cc_start: 0.8712 (tpp) cc_final: 0.8495 (tpt) REVERT: s 206 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8350 (mp0) REVERT: s 227 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8331 (tp30) REVERT: s 277 TYR cc_start: 0.8468 (m-80) cc_final: 0.7985 (m-10) REVERT: s 296 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8897 (tt) REVERT: u 37 ASP cc_start: 0.8636 (t70) cc_final: 0.8268 (t0) REVERT: u 155 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7730 (pp20) REVERT: u 172 MET cc_start: 0.8971 (mtp) cc_final: 0.8372 (mtp) REVERT: v 39 MET cc_start: 0.8246 (tpt) cc_final: 0.7910 (tpp) REVERT: w 272 ASP cc_start: 0.8076 (m-30) cc_final: 0.7678 (m-30) outliers start: 89 outliers final: 54 residues processed: 735 average time/residue: 0.7631 time to fit residues: 672.3898 Evaluate side-chains 740 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 670 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 U residue 32 LEU 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 141 VAL 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 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS 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 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 134 GLN Chi-restraints excluded: chain e residue 72 ASP 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 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 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 140 LEU Chi-restraints excluded: chain l residue 151 SER 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 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 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 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain p residue 159 LYS Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 304 GLN 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 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 208 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 370 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 155 optimal weight: 0.0000 chunk 77 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.091279 restraints weight = 52522.264| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.25 r_work: 0.2827 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 40734 Z= 0.113 Angle : 0.548 11.460 54950 Z= 0.274 Chirality : 0.039 0.300 5931 Planarity : 0.004 0.061 6684 Dihedral : 12.659 171.221 6404 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 1.89 % Allowed : 17.72 % Favored : 80.39 % 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: 2.16 (0.13), residues: 4666 helix: 2.38 (0.09), residues: 2978 sheet: -0.42 (0.96), residues: 35 loop : -0.30 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 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 0.006 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (40726) covalent geometry : angle 0.54749 / 0.27 (54936) SS BOND : bond 0.00314 / 0.19 ( 7) SS BOND : angle 1.50430 / 0.88 ( 14) hydrogen bonds : bond 0.04318 / 2.93 ( 2336) hydrogen bonds : angle 3.99628 / 2.90 ( 6786) Misc. bond : bond 0.00022 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15283.30 seconds wall clock time: 260 minutes 16.86 seconds (15616.86 seconds total)