Starting phenix.real_space_refine on Sat Mar 7 06:23:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vyi_32206/03_2026/7vyi_32206.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vyi_32206/03_2026/7vyi_32206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vyi_32206/03_2026/7vyi_32206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vyi_32206/03_2026/7vyi_32206.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vyi_32206/03_2026/7vyi_32206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vyi_32206/03_2026/7vyi_32206.map" } resolution = 3.1 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 27 5.49 5 S 285 5.16 5 C 25334 2.51 5 N 6186 2.21 5 O 6788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38620 Number of models: 1 Model: "" Number of chains: 41 Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 333 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 7, 'TRANS': 32} Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} 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: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1161 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 129} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1303 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 135} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 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: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 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: 4785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4785 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 28, 'TRANS': 574} Chain: "m" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 951 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "n" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 456 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1530 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 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: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "w" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2563 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "g" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "i" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "j" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 146 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "m" 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: "r" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 354 Unusual residues: {'CDL': 2, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1, ' UQ:plan-11': 1} Unresolved non-hydrogen planarities: 35 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 8.12, per 1000 atoms: 0.21 Number of scatterers: 38620 At special positions: 0 Unit cell: (178.317, 194.43, 137.498, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 285 16.00 P 27 15.00 O 6788 8.00 N 6186 7.00 C 25334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.02 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.04 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 2.0 seconds 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 5 sheets defined 70.7% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'Q' and resid 40 through 45 Processing helix chain 'Q' and resid 46 through 48 No H-bonds generated for 'chain 'Q' and resid 46 through 48' Processing helix chain 'S' and resid 1 through 4 Processing helix chain 'S' and resid 5 through 31 Proline residue: S 19 - end of helix removed outlier: 3.612A pdb=" N ASN S 31 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 56 removed outlier: 3.929A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.023A pdb=" N ASP S 70 " --> pdb=" O GLU S 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 14 Processing helix chain 'U' and resid 16 through 32 removed outlier: 3.662A pdb=" N VAL U 20 " --> pdb=" O GLU U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 37 through 48 removed outlier: 4.242A pdb=" N TYR U 41 " --> pdb=" O PRO U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 78 through 84 Processing helix chain 'V' and resid 3 through 12 removed outlier: 4.194A pdb=" N ILE V 12 " --> pdb=" O LYS V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 44 Processing helix chain 'V' and resid 48 through 82 Processing helix chain 'V' and resid 86 through 106 removed outlier: 4.070A pdb=" N TYR V 90 " --> pdb=" O ASP V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 132 removed outlier: 3.668A pdb=" N THR V 121 " --> pdb=" O TYR V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 98 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 120 through 125 removed outlier: 3.542A pdb=" N LEU W 124 " --> pdb=" O MET W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 129 through 143 removed outlier: 6.339A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 6.164A 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 153 Processing helix chain 'Y' and resid 51 through 76 removed outlier: 3.582A pdb=" N LEU Y 55 " --> pdb=" O THR Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 82 Processing helix chain 'Y' and resid 88 through 92 removed outlier: 3.520A pdb=" N TRP Y 92 " --> pdb=" O PRO Y 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 38 Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.905A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER Z 54 " --> 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 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: 4.133A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) removed outlier: 4.062A 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: 4.028A pdb=" N ASN a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 removed outlier: 3.788A pdb=" N LEU a 178 " --> pdb=" O ASP a 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 26 Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 108 through 112 Processing helix chain 'c' and resid 125 through 150 Processing helix chain 'd' and resid 28 through 41 removed outlier: 4.135A pdb=" N TYR d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 58 removed outlier: 3.545A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 77 Processing helix chain 'd' and resid 81 through 117 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 176 Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.199A 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 removed outlier: 3.567A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 132 removed outlier: 3.519A pdb=" N ALA e 118 " --> pdb=" O MET e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 143 through 147 Processing helix chain 'f' and resid 40 through 74 Processing helix chain 'g' and resid 3 through 7 removed outlier: 4.354A pdb=" N GLY g 6 " --> pdb=" O MET g 3 " (cutoff:3.500A) 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 Processing helix chain 'g' and resid 110 through 114 Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.620A pdb=" N ARG h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 15 through 19 removed outlier: 3.806A pdb=" N MET h 18 " --> pdb=" O ASP h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 45 Processing helix chain 'h' and resid 48 through 56 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 100 removed outlier: 3.910A pdb=" N GLY h 100 " --> pdb=" O HIS h 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 23 Processing helix chain 'i' and resid 25 through 45 removed outlier: 3.573A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 49 through 81 Processing helix chain 'i' and resid 91 through 107 Processing helix chain 'i' and resid 113 through 122 removed outlier: 4.119A 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 150 through 169 Processing helix chain 'i' and resid 170 through 172 No H-bonds generated for 'chain 'i' and resid 170 through 172' Processing helix chain 'i' and resid 174 through 192 Processing helix chain 'i' and resid 197 through 222 removed outlier: 3.649A pdb=" N THR i 201 " --> pdb=" O ASN i 197 " (cutoff:3.500A) Processing helix chain 'i' and resid 226 through 232 Processing helix chain 'i' and resid 233 through 236 Processing helix chain 'i' and resid 237 through 252 Processing helix chain 'i' and resid 259 through 273 removed outlier: 4.401A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 3.527A pdb=" N THR i 280 " --> pdb=" O ILE i 276 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 removed outlier: 3.784A pdb=" N LYS i 314 " --> pdb=" O ASN i 310 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN i 316 " --> pdb=" O LYS i 312 " (cutoff:3.500A) Processing helix chain 'i' and resid 325 through 335 Processing helix chain 'i' and resid 336 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 25 through 27 No H-bonds generated for 'chain 'j' and resid 25 through 27' Processing helix chain 'j' and resid 52 through 73 removed outlier: 4.253A pdb=" N PHE j 56 " --> pdb=" O SER j 52 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 79 Processing helix chain 'j' and resid 83 through 108 Processing helix chain 'k' and resid 2 through 22 removed outlier: 3.615A pdb=" N MET k 6 " --> pdb=" O PRO k 2 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR k 22 " --> pdb=" O GLY k 18 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 51 removed outlier: 3.534A pdb=" N SER k 29 " --> pdb=" O HIS k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 56 Processing helix chain 'k' and resid 57 through 86 removed outlier: 4.658A pdb=" N ILE k 61 " --> pdb=" O ASN k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 89 through 93 Processing helix chain 'l' and resid 2 through 15 removed outlier: 3.882A pdb=" N SER l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 22 Processing helix chain 'l' and resid 23 through 24 No H-bonds generated for 'chain 'l' and resid 23 through 24' Processing helix chain 'l' and resid 25 through 29 Processing helix chain 'l' and resid 31 through 58 removed outlier: 4.330A 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: 3.896A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 134 removed outlier: 3.674A pdb=" N PHE l 117 " --> pdb=" O PHE l 113 " (cutoff:3.500A) Processing helix chain 'l' and resid 136 through 156 removed outlier: 3.543A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 161 through 194 removed outlier: 3.581A pdb=" N ASN l 165 " --> pdb=" O ARG l 161 " (cutoff:3.500A) removed outlier: 3.916A 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: 4.244A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.807A 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 removed outlier: 3.512A pdb=" N PHE l 263 " --> pdb=" O LEU l 259 " (cutoff:3.500A) Processing helix chain 'l' and resid 263 through 268 Processing helix chain 'l' and resid 271 through 293 Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 3.686A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 355 through 359 removed outlier: 3.608A pdb=" N LYS l 358 " --> pdb=" O ASP l 355 " (cutoff:3.500A) Processing helix chain 'l' and resid 366 through 381 removed outlier: 3.523A pdb=" N THR l 370 " --> pdb=" O MET l 366 " (cutoff:3.500A) Processing helix chain 'l' and resid 388 through 401 removed outlier: 4.793A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 405 through 432 removed outlier: 3.562A pdb=" N LEU l 432 " --> pdb=" O PHE l 428 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 472 removed outlier: 3.575A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.173A 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 506 Processing helix chain 'l' and resid 507 through 510 Processing helix chain 'l' and resid 517 through 525 Processing helix chain 'l' and resid 528 through 548 Proline residue: l 537 - end of helix Processing helix chain 'l' and resid 556 through 562 removed outlier: 4.110A 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: 3.590A pdb=" N MET l 599 " --> pdb=" O ILE l 595 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR l 600 " --> pdb=" O MET l 596 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 22 removed outlier: 3.593A pdb=" N SER m 22 " --> pdb=" O VAL m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 48 removed outlier: 3.612A pdb=" N GLY m 29 " --> pdb=" O SER m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 75 removed outlier: 4.128A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 137 through 145 Processing helix chain 'm' and resid 150 through 174 removed outlier: 4.223A pdb=" N GLY m 174 " --> pdb=" O GLU m 170 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 12 Processing helix chain 'n' and resid 15 through 35 removed outlier: 3.933A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 39 Processing helix chain 'o' and resid 15 through 19 Processing helix chain 'o' and resid 26 through 52 Processing helix chain 'o' and resid 62 through 74 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 50 Processing helix chain 'p' and resid 56 through 74 removed outlier: 4.063A pdb=" N GLN p 62 " --> pdb=" O VAL p 58 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU p 64 " --> pdb=" O ALA p 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU p 69 " --> pdb=" O ARG p 65 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR p 73 " --> pdb=" O GLU p 69 " (cutoff:3.500A) Processing helix chain 'p' and resid 94 through 98 removed outlier: 3.614A 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: 3.934A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 144 removed outlier: 3.591A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (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 removed outlier: 4.206A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 22 through 39 Processing helix chain 'r' and resid 40 through 43 Processing helix chain 'r' and resid 61 through 81 removed outlier: 4.005A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 88 through 112 removed outlier: 3.576A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 125 through 136 removed outlier: 3.824A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 171 removed outlier: 4.143A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.768A pdb=" N VAL r 162 " --> pdb=" O LEU r 158 " (cutoff:3.500A) Processing helix chain 'r' and resid 175 through 182 Processing helix chain 'r' and resid 189 through 207 removed outlier: 3.981A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 4.207A 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 247 removed outlier: 4.242A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 258 Processing helix chain 'r' and resid 258 through 278 removed outlier: 4.249A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 281 through 304 Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.758A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 352 through 367 Processing helix chain 'r' and resid 372 through 389 Processing helix chain 'r' and resid 391 through 416 removed outlier: 4.151A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR r 414 " --> pdb=" O MET r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 430 through 448 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 449 through 455 removed outlier: 6.452A pdb=" N LYS r 452 " --> pdb=" O LEU r 449 " (cutoff:3.500A) removed outlier: 3.573A 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: 3.875A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG s 25 " --> pdb=" O THR s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 46 through 57 Processing helix chain 's' and resid 67 through 85 Proline residue: s 75 - end of helix Processing helix chain 's' and resid 100 through 112 Processing helix chain 's' and resid 112 through 123 removed outlier: 4.229A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 3.738A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 3.810A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 178 removed outlier: 3.937A pdb=" N THR s 177 " --> pdb=" O TRP s 173 " (cutoff:3.500A) Processing helix chain 's' and resid 178 through 193 removed outlier: 3.511A pdb=" N ALA s 182 " --> pdb=" O SER s 178 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR s 193 " --> pdb=" O THR s 189 " (cutoff:3.500A) Processing helix chain 's' and resid 218 through 243 Processing helix chain 's' and resid 251 through 277 removed outlier: 4.303A pdb=" N TYR s 255 " --> pdb=" O THR s 251 " (cutoff:3.500A) Processing helix chain 's' and resid 281 through 312 removed outlier: 5.177A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 9 through 14 removed outlier: 3.648A pdb=" N LYS u 14 " --> pdb=" O GLU u 11 " (cutoff:3.500A) Processing helix chain 'u' and resid 21 through 28 Processing helix chain 'u' and resid 28 through 36 Processing helix chain 'u' and resid 36 through 51 removed outlier: 3.528A pdb=" N ASN u 40 " --> pdb=" O CYS u 36 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 55 Processing helix chain 'u' and resid 56 through 78 Processing helix chain 'u' and resid 78 through 92 removed outlier: 3.677A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 100 through 115 Processing helix chain 'v' and resid 3 through 11 Processing helix chain 'v' and resid 26 through 30 removed outlier: 3.843A pdb=" N GLY v 30 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 42 through 50 Processing helix chain 'v' and resid 59 through 73 removed outlier: 3.674A pdb=" N LEU v 63 " --> pdb=" O CYS v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 80 removed outlier: 4.425A pdb=" N CYS v 80 " --> pdb=" O PHE v 77 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 125 removed outlier: 3.515A pdb=" N GLY v 125 " --> pdb=" O GLU v 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 39 through 46 Processing helix chain 'w' and resid 69 through 82 Processing helix chain 'w' and resid 92 through 98 removed outlier: 3.636A pdb=" N SER w 96 " --> pdb=" O HIS w 92 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR w 98 " --> pdb=" O ALA w 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 92 through 98' Processing helix chain 'w' and resid 113 through 120 Processing helix chain 'w' and resid 126 through 154 Processing helix chain 'w' and resid 166 through 176 removed outlier: 3.860A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 196 Processing helix chain 'w' and resid 210 through 222 removed outlier: 3.625A 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: 3.576A pdb=" N LEU w 234 " --> pdb=" O THR w 230 " (cutoff:3.500A) Processing helix chain 'w' and resid 244 through 251 removed outlier: 3.502A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 264 removed outlier: 4.083A pdb=" N GLU w 264 " --> pdb=" O ARG w 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 261 through 264' Processing helix chain 'w' and resid 265 through 276 removed outlier: 3.654A pdb=" N VAL w 269 " --> pdb=" O ASP w 265 " (cutoff:3.500A) Processing helix chain 'w' and resid 281 through 286 removed outlier: 4.271A pdb=" N ASP w 285 " --> pdb=" O GLY w 281 " (cutoff:3.500A) Processing helix chain 'w' and resid 287 through 299 Processing helix chain 'w' and resid 300 through 305 removed outlier: 3.626A pdb=" N VAL w 304 " --> pdb=" O ASN w 300 " (cutoff:3.500A) Processing helix chain 'w' and resid 306 through 310 removed outlier: 3.881A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE w 310 " --> pdb=" O TYR w 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 310' Processing helix chain 'w' and resid 320 through 333 Processing helix chain 'w' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'U' and resid 57 through 58 removed outlier: 6.392A 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 99 Processing sheet with id=AA3, first strand: chain 'b' and resid 97 through 99 removed outlier: 5.399A pdb=" N SER l 64 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE l 80 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TRP l 66 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU l 76 " --> pdb=" O TRP l 68 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR l 70 " --> pdb=" O VAL l 74 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL l 74 " --> pdb=" O THR l 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'w' and resid 84 through 85 removed outlier: 6.451A pdb=" N ARG w 84 " --> pdb=" O VAL w 158 " (cutoff:3.500A) 2300 hydrogen bonds defined for protein. 6705 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: 8.24 Time building geometry restraints manager: 4.45 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: 5862 1.31 - 1.44: 10766 1.44 - 1.57: 22354 1.57 - 1.70: 126 1.70 - 1.83: 515 Bond restraints: 39623 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C18 UQ s 401 " pdb=" C19 UQ s 401 " 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 401 " pdb=" C14 UQ s 401 " ideal model delta sigma weight residual 1.335 1.549 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C8 UQ s 401 " pdb=" C9 UQ s 401 " ideal model delta sigma weight residual 1.334 1.541 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C4' ADP w 401 " pdb=" O4' ADP w 401 " ideal model delta sigma weight residual 1.426 1.618 -0.192 2.00e-02 2.50e+03 9.26e+01 ... (remaining 39618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 53010 3.37 - 6.73: 437 6.73 - 10.10: 78 10.10 - 13.47: 22 13.47 - 16.84: 9 Bond angle restraints: 53556 Sorted by residual: angle pdb=" C TYR c 75 " pdb=" N PRO c 76 " pdb=" CA PRO c 76 " ideal model delta sigma weight residual 119.85 130.15 -10.30 1.01e+00 9.80e-01 1.04e+02 angle pdb=" C PHE c 37 " pdb=" N PRO c 38 " pdb=" CA PRO c 38 " ideal model delta sigma weight residual 119.89 127.10 -7.21 1.02e+00 9.61e-01 4.99e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.53 -9.20 1.32e+00 5.72e-01 4.85e+01 angle pdb=" C11 CDL i 401 " pdb=" CA5 CDL i 401 " pdb=" OA6 CDL i 401 " ideal model delta sigma weight residual 111.33 120.31 -8.98 1.32e+00 5.72e-01 4.61e+01 angle pdb=" C51 CDL g 202 " pdb=" CB5 CDL g 202 " pdb=" OB6 CDL g 202 " ideal model delta sigma weight residual 111.33 120.19 -8.86 1.32e+00 5.72e-01 4.49e+01 ... (remaining 53551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.24: 22951 32.24 - 64.49: 992 64.49 - 96.73: 94 96.73 - 128.98: 17 128.98 - 161.22: 16 Dihedral angle restraints: 24070 sinusoidal: 10432 harmonic: 13638 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 87.62 -147.61 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O2A ADP w 401 " pdb=" O3A ADP w 401 " pdb=" PA ADP w 401 " pdb=" PB ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 -167.08 107.08 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" O1B ADP w 401 " pdb=" O3A ADP w 401 " pdb=" PB ADP w 401 " pdb=" PA ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 35.96 -95.97 1 2.00e+01 2.50e-03 2.65e+01 ... (remaining 24067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5347 0.071 - 0.142: 460 0.142 - 0.213: 16 0.213 - 0.284: 1 0.284 - 0.356: 7 Chirality restraints: 5831 Sorted by residual: chirality pdb=" CA LEU w 246 " pdb=" N LEU w 246 " pdb=" C LEU w 246 " pdb=" CB LEU w 246 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C6 PLX g 201 " pdb=" C7 PLX g 201 " pdb=" O6 PLX g 201 " pdb=" O7 PLX g 201 " both_signs ideal model delta sigma weight residual False 2.01 2.34 -0.33 2.00e-01 2.50e+01 2.65e+00 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 -0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 5828 not shown) Planarity restraints: 6553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 401 " -0.088 2.00e-02 2.50e+03 4.45e-01 2.48e+03 pdb=" C11 UQ s 401 " -0.412 2.00e-02 2.50e+03 pdb=" C7 UQ s 401 " -0.521 2.00e-02 2.50e+03 pdb=" C8 UQ s 401 " 0.613 2.00e-02 2.50e+03 pdb=" C9 UQ s 401 " 0.408 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 401 " -0.158 2.00e-02 2.50e+03 2.05e-01 5.23e+02 pdb=" C18 UQ s 401 " 0.092 2.00e-02 2.50e+03 pdb=" C19 UQ s 401 " 0.347 2.00e-02 2.50e+03 pdb=" C20 UQ s 401 " -0.051 2.00e-02 2.50e+03 pdb=" C21 UQ s 401 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 401 " 0.155 2.00e-02 2.50e+03 2.03e-01 5.15e+02 pdb=" C13 UQ s 401 " -0.084 2.00e-02 2.50e+03 pdb=" C14 UQ s 401 " -0.348 2.00e-02 2.50e+03 pdb=" C15 UQ s 401 " 0.050 2.00e-02 2.50e+03 pdb=" C16 UQ s 401 " 0.228 2.00e-02 2.50e+03 ... (remaining 6550 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2475 2.74 - 3.28: 39056 3.28 - 3.82: 65568 3.82 - 4.36: 78198 4.36 - 4.90: 136141 Nonbonded interactions: 321438 Sorted by model distance: nonbonded pdb=" O ILE l 556 " pdb=" OG1 THR l 560 " model vdw 2.196 3.040 nonbonded pdb=" OE2 GLU r 123 " pdb=" OG SER r 157 " model vdw 2.201 3.040 nonbonded pdb=" O ASP Q 68 " pdb=" ND2 ASN i 49 " model vdw 2.206 3.120 nonbonded pdb=" OD1 ASP X 111 " pdb=" N SER X 112 " model vdw 2.208 3.120 nonbonded pdb=" OG SER w 123 " pdb=" OD1 ASP w 125 " model vdw 2.216 3.040 ... (remaining 321433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.760 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.007 0.278 39630 Z= 0.401 Angle : 0.808 16.836 53568 Z= 0.400 Chirality : 0.042 0.356 5831 Planarity : 0.008 0.445 6553 Dihedral : 17.740 161.221 15238 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 0.32 % Allowed : 0.35 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.83 (0.13), residues: 4586 helix: 2.12 (0.10), residues: 2915 sheet: -0.56 (1.21), residues: 23 loop : -0.41 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 81 TYR 0.042 0.001 TYR w 129 PHE 0.031 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.005 0.001 HIS r 220 Details of bonding type rmsd covalent geometry : bond 0.00684 (39623) covalent geometry : angle 0.80763 (53556) SS BOND : bond 0.00495 ( 6) SS BOND : angle 1.73293 ( 12) hydrogen bonds : bond 0.13124 ( 2300) hydrogen bonds : angle 5.28958 ( 6705) Misc. bond : bond 0.27784 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 837 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: V 44 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6918 (pttt) REVERT: V 60 THR cc_start: 0.8173 (m) cc_final: 0.7951 (m) REVERT: V 100 THR cc_start: 0.8608 (p) cc_final: 0.8403 (p) REVERT: X 74 LEU cc_start: 0.8641 (pt) cc_final: 0.8367 (pt) REVERT: Y 65 MET cc_start: 0.8746 (tmm) cc_final: 0.8458 (ttt) REVERT: Z 61 VAL cc_start: 0.8669 (m) cc_final: 0.8342 (p) REVERT: b 76 LEU cc_start: 0.9162 (tp) cc_final: 0.8954 (tp) REVERT: k 27 MET cc_start: 0.7722 (tpp) cc_final: 0.7424 (tpp) REVERT: m 5 ILE cc_start: 0.7961 (tt) cc_final: 0.7684 (tt) REVERT: p 64 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8479 (tt) REVERT: p 65 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7480 (ttt180) REVERT: p 66 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: s 24 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: s 121 TRP cc_start: 0.7525 (t60) cc_final: 0.7261 (t60) outliers start: 13 outliers final: 5 residues processed: 846 average time/residue: 0.2359 time to fit residues: 325.6077 Evaluate side-chains 753 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 744 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 103 GLU Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 62 GLN Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 65 ARG Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 39 HIS Y 46 GLN d 134 GLN e 132 ASN i 36 ASN l 135 ASN ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 447 ASN n 14 HIS o 123 GLN p 12 HIS p 33 HIS p 66 GLN r 43 ASN r 103 GLN u 16 GLN u 77 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099256 restraints weight = 54318.319| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.44 r_work: 0.2926 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 39630 Z= 0.154 Angle : 0.595 13.919 53568 Z= 0.295 Chirality : 0.042 0.192 5831 Planarity : 0.004 0.050 6553 Dihedral : 15.960 149.273 6188 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 1.09 % Allowed : 7.02 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.13), residues: 4586 helix: 2.28 (0.10), residues: 2951 sheet: -0.38 (1.28), residues: 23 loop : -0.33 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG w 175 TYR 0.033 0.001 TYR w 129 PHE 0.033 0.002 PHE i 292 TRP 0.022 0.001 TRP u 86 HIS 0.010 0.001 HIS h 27 Details of bonding type rmsd covalent geometry : bond 0.00358 (39623) covalent geometry : angle 0.59474 (53556) SS BOND : bond 0.00369 ( 6) SS BOND : angle 1.64746 ( 12) hydrogen bonds : bond 0.04835 ( 2300) hydrogen bonds : angle 4.14021 ( 6705) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 770 time to evaluate : 1.482 Fit side-chains revert: symmetry clash REVERT: U 10 LYS cc_start: 0.8507 (tttm) cc_final: 0.8255 (ttpt) REVERT: U 83 ASN cc_start: 0.7782 (m-40) cc_final: 0.7412 (m-40) REVERT: V 25 SER cc_start: 0.8360 (m) cc_final: 0.7909 (p) REVERT: V 44 LYS cc_start: 0.7326 (mmtt) cc_final: 0.7016 (pttt) REVERT: X 74 LEU cc_start: 0.8864 (pt) cc_final: 0.8538 (pt) REVERT: X 105 MET cc_start: 0.8075 (mpp) cc_final: 0.7748 (mpp) REVERT: Z 61 VAL cc_start: 0.8710 (m) cc_final: 0.8300 (p) REVERT: a 127 ASP cc_start: 0.8667 (m-30) cc_final: 0.7975 (t0) REVERT: e 145 ASN cc_start: 0.8274 (m110) cc_final: 0.8052 (m-40) REVERT: f 63 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7653 (mmtt) REVERT: i 157 MET cc_start: 0.9316 (mtp) cc_final: 0.9106 (mtp) REVERT: i 281 LEU cc_start: 0.8590 (mp) cc_final: 0.8374 (mp) REVERT: i 282 MET cc_start: 0.8714 (mtt) cc_final: 0.8509 (mtp) REVERT: k 27 MET cc_start: 0.7971 (tpp) cc_final: 0.7601 (tpp) REVERT: k 85 TYR cc_start: 0.8311 (m-80) cc_final: 0.8092 (m-80) REVERT: l 128 MET cc_start: 0.8924 (tpt) cc_final: 0.8352 (tpt) REVERT: l 252 MET cc_start: 0.9098 (ttp) cc_final: 0.8569 (ttp) REVERT: m 173 ARG cc_start: 0.8353 (tpp80) cc_final: 0.8051 (ttm-80) REVERT: p 43 LEU cc_start: 0.9023 (tt) cc_final: 0.8707 (mt) REVERT: p 64 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8278 (tp) REVERT: v 48 ASP cc_start: 0.8035 (m-30) cc_final: 0.7561 (m-30) outliers start: 44 outliers final: 27 residues processed: 789 average time/residue: 0.2284 time to fit residues: 294.1574 Evaluate side-chains 745 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 717 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 153 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 443 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 389 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 410 optimal weight: 0.4980 chunk 274 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 46 GLN l 72 GLN l 226 GLN ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN p 33 HIS r 26 ASN r 43 ASN r 103 GLN u 16 GLN u 77 HIS w 127 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.101437 restraints weight = 54098.302| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.44 r_work: 0.2966 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39630 Z= 0.115 Angle : 0.534 12.730 53568 Z= 0.266 Chirality : 0.039 0.171 5831 Planarity : 0.004 0.052 6553 Dihedral : 14.785 152.708 6165 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 1.01 % Allowed : 9.17 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.13), residues: 4586 helix: 2.41 (0.09), residues: 2955 sheet: -0.17 (1.31), residues: 23 loop : -0.30 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG r 340 TYR 0.030 0.001 TYR w 129 PHE 0.028 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.008 0.001 HIS r 83 Details of bonding type rmsd covalent geometry : bond 0.00253 (39623) covalent geometry : angle 0.53411 (53556) SS BOND : bond 0.00356 ( 6) SS BOND : angle 1.36032 ( 12) hydrogen bonds : bond 0.04362 ( 2300) hydrogen bonds : angle 3.95408 ( 6705) Misc. bond : bond 0.00153 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 758 time to evaluate : 0.915 Fit side-chains REVERT: U 83 ASN cc_start: 0.7835 (m-40) cc_final: 0.7460 (m-40) REVERT: V 44 LYS cc_start: 0.7454 (mmtt) cc_final: 0.7150 (pttt) REVERT: X 74 LEU cc_start: 0.8715 (pt) cc_final: 0.8423 (pt) REVERT: X 105 MET cc_start: 0.8116 (mpp) cc_final: 0.7913 (mpp) REVERT: Z 61 VAL cc_start: 0.8701 (m) cc_final: 0.8288 (p) REVERT: a 127 ASP cc_start: 0.8713 (m-30) cc_final: 0.8000 (t0) REVERT: c 179 GLU cc_start: 0.7086 (pm20) cc_final: 0.6623 (pt0) REVERT: e 145 ASN cc_start: 0.8314 (m110) cc_final: 0.8086 (m-40) REVERT: f 63 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7591 (mmtt) REVERT: g 36 MET cc_start: 0.8773 (mmm) cc_final: 0.8450 (mmm) REVERT: i 281 LEU cc_start: 0.8518 (mp) cc_final: 0.8307 (mp) REVERT: i 282 MET cc_start: 0.8708 (mtt) cc_final: 0.8421 (mtp) REVERT: k 27 MET cc_start: 0.7866 (tpp) cc_final: 0.7600 (tpp) REVERT: l 128 MET cc_start: 0.8896 (tpt) cc_final: 0.8360 (tpt) REVERT: l 186 MET cc_start: 0.9096 (ttm) cc_final: 0.8768 (ttp) REVERT: l 475 MET cc_start: 0.7696 (mtt) cc_final: 0.7312 (mmt) REVERT: m 137 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8415 (t) REVERT: m 173 ARG cc_start: 0.8349 (tpp80) cc_final: 0.8090 (ttm-80) REVERT: p 43 LEU cc_start: 0.8960 (tt) cc_final: 0.8759 (mt) REVERT: p 49 ASP cc_start: 0.8179 (t0) cc_final: 0.7714 (t0) REVERT: p 64 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8326 (tp) REVERT: v 48 ASP cc_start: 0.8033 (m-30) cc_final: 0.7706 (m-30) outliers start: 41 outliers final: 28 residues processed: 778 average time/residue: 0.2276 time to fit residues: 289.6628 Evaluate side-chains 738 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 708 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 77 CYS Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 219 optimal weight: 0.0670 chunk 177 optimal weight: 1.9990 chunk 412 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 chunk 341 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 363 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 44 GLN Y 46 GLN a 109 HIS d 124 ASN l 205 ASN l 320 ASN l 400 ASN o 123 GLN r 43 ASN r 103 GLN r 169 ASN u 16 GLN u 77 HIS v 43 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.100474 restraints weight = 53961.244| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.43 r_work: 0.2943 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39630 Z= 0.125 Angle : 0.536 12.051 53568 Z= 0.267 Chirality : 0.040 0.174 5831 Planarity : 0.004 0.050 6553 Dihedral : 14.126 144.891 6165 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 1.36 % Allowed : 10.25 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 2.24 (0.13), residues: 4586 helix: 2.43 (0.09), residues: 2961 sheet: -0.08 (1.36), residues: 23 loop : -0.30 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG w 175 TYR 0.035 0.001 TYR w 129 PHE 0.030 0.001 PHE i 292 TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS r 83 Details of bonding type rmsd covalent geometry : bond 0.00286 (39623) covalent geometry : angle 0.53561 (53556) SS BOND : bond 0.00350 ( 6) SS BOND : angle 1.44818 ( 12) hydrogen bonds : bond 0.04375 ( 2300) hydrogen bonds : angle 3.91839 ( 6705) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 733 time to evaluate : 1.413 Fit side-chains REVERT: S 44 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8244 (pm20) REVERT: V 17 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6366 (mt-10) REVERT: V 44 LYS cc_start: 0.7437 (mmtt) cc_final: 0.7167 (pttt) REVERT: X 74 LEU cc_start: 0.8697 (pt) cc_final: 0.8392 (pt) REVERT: X 146 ASP cc_start: 0.8073 (m-30) cc_final: 0.7871 (m-30) REVERT: Y 46 GLN cc_start: 0.8739 (mt0) cc_final: 0.8520 (mt0) REVERT: Z 61 VAL cc_start: 0.8686 (m) cc_final: 0.8287 (p) REVERT: a 127 ASP cc_start: 0.8660 (m-30) cc_final: 0.7958 (t0) REVERT: a 130 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8684 (mp0) REVERT: c 148 GLU cc_start: 0.8480 (tp30) cc_final: 0.8260 (tp30) REVERT: g 36 MET cc_start: 0.8735 (mmm) cc_final: 0.8474 (mmm) REVERT: i 281 LEU cc_start: 0.8562 (mp) cc_final: 0.8352 (mp) REVERT: i 282 MET cc_start: 0.8745 (mtt) cc_final: 0.8458 (mtp) REVERT: j 105 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8578 (tp30) REVERT: k 27 MET cc_start: 0.7951 (tpp) cc_final: 0.7642 (tpp) REVERT: l 340 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8800 (m-80) REVERT: l 475 MET cc_start: 0.7695 (mtt) cc_final: 0.7311 (mmt) REVERT: m 137 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8482 (t) REVERT: p 49 ASP cc_start: 0.8257 (t0) cc_final: 0.7844 (t0) REVERT: p 64 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8330 (tp) REVERT: v 48 ASP cc_start: 0.8100 (m-30) cc_final: 0.7653 (m-30) REVERT: w 120 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7460 (p0) outliers start: 55 outliers final: 36 residues processed: 768 average time/residue: 0.2279 time to fit residues: 286.9977 Evaluate side-chains 746 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 702 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 120 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 177 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 402 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 223 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 123 GLN r 43 ASN r 103 GLN r 220 HIS u 16 GLN u 77 HIS w 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101068 restraints weight = 54016.489| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.40 r_work: 0.2950 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39630 Z= 0.116 Angle : 0.526 11.136 53568 Z= 0.263 Chirality : 0.039 0.186 5831 Planarity : 0.004 0.050 6553 Dihedral : 13.688 136.797 6165 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 1.56 % Allowed : 10.75 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 2.32 (0.13), residues: 4586 helix: 2.50 (0.09), residues: 2955 sheet: -0.07 (1.39), residues: 23 loop : -0.27 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG w 175 TYR 0.039 0.001 TYR w 129 PHE 0.030 0.001 PHE i 292 TRP 0.022 0.001 TRP w 353 HIS 0.007 0.001 HIS r 83 Details of bonding type rmsd covalent geometry : bond 0.00260 (39623) covalent geometry : angle 0.52561 (53556) SS BOND : bond 0.00510 ( 6) SS BOND : angle 1.46236 ( 12) hydrogen bonds : bond 0.04257 ( 2300) hydrogen bonds : angle 3.88252 ( 6705) Misc. bond : bond 0.00070 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 733 time to evaluate : 1.409 Fit side-chains REVERT: V 44 LYS cc_start: 0.7521 (mmtt) cc_final: 0.7193 (pttt) REVERT: V 106 ARG cc_start: 0.6858 (tpm170) cc_final: 0.4610 (mtt90) REVERT: X 74 LEU cc_start: 0.8702 (pt) cc_final: 0.8407 (pt) REVERT: Z 61 VAL cc_start: 0.8685 (m) cc_final: 0.8272 (p) REVERT: a 127 ASP cc_start: 0.8748 (m-30) cc_final: 0.8012 (t0) REVERT: a 130 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: c 148 GLU cc_start: 0.8471 (tp30) cc_final: 0.8239 (tp30) REVERT: i 281 LEU cc_start: 0.8561 (mp) cc_final: 0.8358 (mp) REVERT: i 282 MET cc_start: 0.8738 (mtt) cc_final: 0.8406 (mtp) REVERT: j 105 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8687 (tp30) REVERT: k 26 LEU cc_start: 0.7971 (tp) cc_final: 0.7754 (tp) REVERT: k 27 MET cc_start: 0.7931 (tpp) cc_final: 0.7674 (tpp) REVERT: k 59 MET cc_start: 0.8549 (tmm) cc_final: 0.8332 (tmm) REVERT: l 340 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8831 (m-80) REVERT: l 475 MET cc_start: 0.7730 (mtt) cc_final: 0.7213 (mmt) REVERT: m 31 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8191 (mp) REVERT: m 137 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8510 (t) REVERT: m 169 MET cc_start: 0.8502 (mmm) cc_final: 0.8287 (mtp) REVERT: m 170 GLU cc_start: 0.8727 (tp30) cc_final: 0.8509 (tp30) REVERT: m 173 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8004 (ttm170) REVERT: p 49 ASP cc_start: 0.8263 (t0) cc_final: 0.7905 (t0) REVERT: p 64 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8230 (tp) REVERT: s 121 TRP cc_start: 0.7981 (t60) cc_final: 0.7502 (t60) REVERT: v 48 ASP cc_start: 0.8125 (m-30) cc_final: 0.7664 (m-30) REVERT: w 248 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6875 (mm-30) outliers start: 63 outliers final: 44 residues processed: 774 average time/residue: 0.2256 time to fit residues: 286.3517 Evaluate side-chains 752 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 702 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 43 SER Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 8 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 321 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 357 optimal weight: 3.9990 chunk 257 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 123 GLN r 43 ASN r 44 GLN r 103 GLN u 16 GLN u 77 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.100292 restraints weight = 54097.686| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.39 r_work: 0.2947 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39630 Z= 0.122 Angle : 0.529 10.475 53568 Z= 0.265 Chirality : 0.039 0.200 5831 Planarity : 0.004 0.050 6553 Dihedral : 13.269 126.939 6165 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 1.73 % Allowed : 11.19 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 2.32 (0.13), residues: 4586 helix: 2.49 (0.09), residues: 2964 sheet: -0.38 (1.37), residues: 23 loop : -0.27 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG w 175 TYR 0.038 0.001 TYR w 129 PHE 0.031 0.001 PHE i 292 TRP 0.022 0.001 TRP w 353 HIS 0.007 0.001 HIS r 83 Details of bonding type rmsd covalent geometry : bond 0.00278 (39623) covalent geometry : angle 0.52876 (53556) SS BOND : bond 0.00367 ( 6) SS BOND : angle 1.48030 ( 12) hydrogen bonds : bond 0.04288 ( 2300) hydrogen bonds : angle 3.88001 ( 6705) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 724 time to evaluate : 1.274 Fit side-chains REVERT: V 17 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6311 (mt-10) REVERT: V 44 LYS cc_start: 0.7581 (mmtt) cc_final: 0.7235 (pttt) REVERT: V 62 THR cc_start: 0.7777 (m) cc_final: 0.7574 (m) REVERT: V 106 ARG cc_start: 0.6918 (tpm170) cc_final: 0.4692 (mtt90) REVERT: X 74 LEU cc_start: 0.8719 (pt) cc_final: 0.8400 (pt) REVERT: Y 46 GLN cc_start: 0.8772 (mt0) cc_final: 0.8545 (mt0) REVERT: Z 61 VAL cc_start: 0.8678 (m) cc_final: 0.8260 (p) REVERT: a 127 ASP cc_start: 0.8688 (m-30) cc_final: 0.8001 (t0) REVERT: a 130 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: c 148 GLU cc_start: 0.8478 (tp30) cc_final: 0.8257 (tp30) REVERT: g 36 MET cc_start: 0.8794 (mmm) cc_final: 0.8358 (mmm) REVERT: i 187 MET cc_start: 0.9097 (mmp) cc_final: 0.8790 (mmp) REVERT: i 281 LEU cc_start: 0.8579 (mp) cc_final: 0.8373 (mp) REVERT: i 282 MET cc_start: 0.8765 (mtt) cc_final: 0.8468 (mtp) REVERT: k 27 MET cc_start: 0.7928 (tpp) cc_final: 0.7709 (tpp) REVERT: l 340 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: m 31 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8188 (mp) REVERT: m 137 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8558 (t) REVERT: m 169 MET cc_start: 0.8509 (mmm) cc_final: 0.8298 (mtp) REVERT: p 49 ASP cc_start: 0.8273 (t0) cc_final: 0.7966 (t0) REVERT: p 64 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8278 (tp) REVERT: s 121 TRP cc_start: 0.7988 (t60) cc_final: 0.7510 (t60) REVERT: v 48 ASP cc_start: 0.8162 (m-30) cc_final: 0.7707 (m-30) REVERT: w 120 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7354 (p0) outliers start: 70 outliers final: 47 residues processed: 771 average time/residue: 0.2308 time to fit residues: 291.1894 Evaluate side-chains 755 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 701 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 43 SER Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 558 LEU Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 120 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 262 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 23 optimal weight: 0.9980 chunk 343 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 417 optimal weight: 0.8980 chunk 403 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 422 optimal weight: 0.0040 chunk 60 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 447 ASN o 123 GLN r 43 ASN r 44 GLN r 103 GLN r 220 HIS r 293 HIS u 16 GLN w 235 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.101537 restraints weight = 53869.406| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.42 r_work: 0.2964 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 39630 Z= 0.111 Angle : 0.522 9.433 53568 Z= 0.261 Chirality : 0.039 0.189 5831 Planarity : 0.004 0.050 6553 Dihedral : 12.778 123.662 6165 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 1.70 % Allowed : 11.66 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 2.39 (0.13), residues: 4586 helix: 2.52 (0.09), residues: 2965 sheet: 0.02 (1.29), residues: 25 loop : -0.21 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG w 175 TYR 0.035 0.001 TYR w 129 PHE 0.029 0.001 PHE i 292 TRP 0.024 0.001 TRP w 353 HIS 0.007 0.001 HIS r 83 Details of bonding type rmsd covalent geometry : bond 0.00243 (39623) covalent geometry : angle 0.52129 (53556) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.41119 ( 12) hydrogen bonds : bond 0.04060 ( 2300) hydrogen bonds : angle 3.83788 ( 6705) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 742 time to evaluate : 1.407 Fit side-chains REVERT: U 51 TYR cc_start: 0.8924 (m-80) cc_final: 0.8647 (m-80) REVERT: V 25 SER cc_start: 0.8382 (m) cc_final: 0.7938 (p) REVERT: V 44 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7242 (pttt) REVERT: V 106 ARG cc_start: 0.6673 (tpm170) cc_final: 0.4517 (mtt90) REVERT: X 74 LEU cc_start: 0.8711 (pt) cc_final: 0.8409 (pt) REVERT: Y 46 GLN cc_start: 0.8726 (mt0) cc_final: 0.8475 (mt0) REVERT: Z 61 VAL cc_start: 0.8681 (m) cc_final: 0.8255 (p) REVERT: a 127 ASP cc_start: 0.8760 (m-30) cc_final: 0.8028 (t0) REVERT: a 130 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: c 148 GLU cc_start: 0.8420 (tp30) cc_final: 0.8183 (tp30) REVERT: g 36 MET cc_start: 0.8776 (mmm) cc_final: 0.8395 (mmm) REVERT: i 187 MET cc_start: 0.9079 (mmp) cc_final: 0.8805 (mmp) REVERT: k 27 MET cc_start: 0.7965 (tpp) cc_final: 0.7713 (tpp) REVERT: l 340 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8843 (m-80) REVERT: l 475 MET cc_start: 0.7657 (mtt) cc_final: 0.7320 (mmt) REVERT: l 484 LEU cc_start: 0.7951 (mt) cc_final: 0.7584 (mt) REVERT: m 31 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8253 (mp) REVERT: m 137 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8610 (t) REVERT: p 49 ASP cc_start: 0.8259 (t0) cc_final: 0.8001 (t0) REVERT: p 64 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8330 (tp) REVERT: r 398 MET cc_start: 0.8327 (mmp) cc_final: 0.7836 (mtm) REVERT: s 121 TRP cc_start: 0.7995 (t60) cc_final: 0.7505 (t60) REVERT: v 48 ASP cc_start: 0.8171 (m-30) cc_final: 0.7698 (m-30) REVERT: v 76 ASN cc_start: 0.8048 (t0) cc_final: 0.7594 (p0) REVERT: w 120 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7329 (p0) outliers start: 69 outliers final: 46 residues processed: 786 average time/residue: 0.2290 time to fit residues: 292.9741 Evaluate side-chains 764 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 712 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 43 SER Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 120 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 262 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 55 optimal weight: 1.9990 chunk 383 optimal weight: 6.9990 chunk 449 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 319 optimal weight: 0.0970 chunk 51 optimal weight: 0.0050 chunk 275 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 451 optimal weight: 0.0010 chunk 112 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 123 GLN r 43 ASN u 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.101615 restraints weight = 53851.776| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.42 r_work: 0.2973 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39630 Z= 0.109 Angle : 0.523 8.856 53568 Z= 0.261 Chirality : 0.039 0.203 5831 Planarity : 0.004 0.050 6553 Dihedral : 12.427 120.231 6165 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 1.63 % Allowed : 12.01 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 2.45 (0.13), residues: 4586 helix: 2.56 (0.09), residues: 2966 sheet: 0.03 (1.30), residues: 25 loop : -0.16 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG m 173 TYR 0.032 0.001 TYR w 129 PHE 0.029 0.001 PHE i 292 TRP 0.026 0.001 TRP w 353 HIS 0.007 0.001 HIS r 83 Details of bonding type rmsd covalent geometry : bond 0.00238 (39623) covalent geometry : angle 0.52224 (53556) SS BOND : bond 0.00358 ( 6) SS BOND : angle 1.42492 ( 12) hydrogen bonds : bond 0.03979 ( 2300) hydrogen bonds : angle 3.82428 ( 6705) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 742 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: U 51 TYR cc_start: 0.8926 (m-80) cc_final: 0.8652 (m-80) REVERT: V 25 SER cc_start: 0.8342 (m) cc_final: 0.7918 (p) REVERT: V 44 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7233 (pttt) REVERT: V 81 ARG cc_start: 0.8457 (mtp-110) cc_final: 0.8089 (mtp-110) REVERT: V 106 ARG cc_start: 0.6589 (tpm170) cc_final: 0.4450 (mtt90) REVERT: W 121 MET cc_start: 0.8500 (tpp) cc_final: 0.8204 (tpp) REVERT: X 74 LEU cc_start: 0.8701 (pt) cc_final: 0.8401 (pt) REVERT: Y 46 GLN cc_start: 0.8675 (mt0) cc_final: 0.8424 (mt0) REVERT: Z 61 VAL cc_start: 0.8686 (m) cc_final: 0.8249 (p) REVERT: a 127 ASP cc_start: 0.8766 (m-30) cc_final: 0.8043 (t0) REVERT: c 81 ARG cc_start: 0.8912 (mmt90) cc_final: 0.8680 (mmm-85) REVERT: c 148 GLU cc_start: 0.8441 (tp30) cc_final: 0.8211 (tp30) REVERT: i 187 MET cc_start: 0.9075 (mmp) cc_final: 0.8795 (mmp) REVERT: k 26 LEU cc_start: 0.7793 (tp) cc_final: 0.7512 (tp) REVERT: l 186 MET cc_start: 0.9103 (ttm) cc_final: 0.8776 (ttp) REVERT: l 340 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8878 (m-80) REVERT: l 475 MET cc_start: 0.7677 (mtt) cc_final: 0.7320 (mmt) REVERT: l 484 LEU cc_start: 0.7968 (mt) cc_final: 0.7390 (mt) REVERT: m 31 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8208 (mp) REVERT: m 137 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8667 (t) REVERT: m 141 MET cc_start: 0.7979 (mmm) cc_final: 0.7663 (mmm) REVERT: o 31 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8752 (tttm) REVERT: p 49 ASP cc_start: 0.8227 (t0) cc_final: 0.8012 (t0) REVERT: r 398 MET cc_start: 0.8344 (mmp) cc_final: 0.8097 (mmm) REVERT: s 121 TRP cc_start: 0.7987 (t60) cc_final: 0.7501 (t60) REVERT: s 170 GLU cc_start: 0.7639 (tt0) cc_final: 0.7347 (tt0) REVERT: v 48 ASP cc_start: 0.8165 (m-30) cc_final: 0.7847 (m-30) REVERT: v 76 ASN cc_start: 0.7981 (t0) cc_final: 0.7716 (p0) REVERT: v 105 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: w 120 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7223 (p0) outliers start: 66 outliers final: 48 residues processed: 785 average time/residue: 0.2283 time to fit residues: 292.9538 Evaluate side-chains 766 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 713 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 43 SER Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 558 LEU Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 120 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 386 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 401 optimal weight: 0.3980 chunk 272 optimal weight: 0.6980 chunk 290 optimal weight: 0.9980 chunk 293 optimal weight: 1.9990 chunk 314 optimal weight: 0.0020 chunk 337 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 108 GLN o 123 GLN r 43 ASN r 220 HIS u 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.102458 restraints weight = 54008.298| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.43 r_work: 0.2984 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 39630 Z= 0.108 Angle : 0.528 14.780 53568 Z= 0.263 Chirality : 0.039 0.203 5831 Planarity : 0.004 0.050 6553 Dihedral : 12.216 119.360 6163 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 1.38 % Allowed : 12.45 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 2.48 (0.13), residues: 4586 helix: 2.60 (0.09), residues: 2959 sheet: 0.01 (1.29), residues: 25 loop : -0.17 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG r 340 TYR 0.029 0.001 TYR w 129 PHE 0.029 0.001 PHE i 292 TRP 0.025 0.001 TRP w 353 HIS 0.007 0.001 HIS r 83 Details of bonding type rmsd covalent geometry : bond 0.00235 (39623) covalent geometry : angle 0.52742 (53556) SS BOND : bond 0.00337 ( 6) SS BOND : angle 1.36395 ( 12) hydrogen bonds : bond 0.03911 ( 2300) hydrogen bonds : angle 3.82059 ( 6705) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 726 time to evaluate : 1.379 Fit side-chains REVERT: U 51 TYR cc_start: 0.8925 (m-80) cc_final: 0.8653 (m-80) REVERT: V 44 LYS cc_start: 0.7587 (mmtt) cc_final: 0.7234 (pttt) REVERT: V 106 ARG cc_start: 0.6543 (tpm170) cc_final: 0.4336 (mtt90) REVERT: X 74 LEU cc_start: 0.8691 (pt) cc_final: 0.8384 (pt) REVERT: X 146 ASP cc_start: 0.7990 (m-30) cc_final: 0.7580 (m-30) REVERT: Y 76 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7656 (p0) REVERT: Z 61 VAL cc_start: 0.8689 (m) cc_final: 0.8256 (p) REVERT: a 127 ASP cc_start: 0.8772 (m-30) cc_final: 0.8061 (t0) REVERT: b 16 ARG cc_start: 0.8191 (mtp180) cc_final: 0.7845 (mtm-85) REVERT: c 81 ARG cc_start: 0.8901 (mmt90) cc_final: 0.8676 (mmm-85) REVERT: c 148 GLU cc_start: 0.8440 (tp30) cc_final: 0.8208 (tp30) REVERT: i 281 LEU cc_start: 0.8460 (mt) cc_final: 0.8249 (mp) REVERT: k 26 LEU cc_start: 0.7804 (tp) cc_final: 0.7502 (tp) REVERT: l 186 MET cc_start: 0.9110 (ttm) cc_final: 0.8815 (ttp) REVERT: l 340 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8857 (m-80) REVERT: l 475 MET cc_start: 0.7602 (mtt) cc_final: 0.7249 (mmt) REVERT: l 484 LEU cc_start: 0.8035 (mt) cc_final: 0.7440 (mt) REVERT: m 1 MET cc_start: 0.2970 (tmm) cc_final: 0.2255 (tpt) REVERT: m 31 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8180 (mp) REVERT: m 137 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8673 (t) REVERT: m 141 MET cc_start: 0.7954 (mmm) cc_final: 0.7654 (mmm) REVERT: m 173 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8236 (ttm110) REVERT: p 49 ASP cc_start: 0.8224 (t0) cc_final: 0.8002 (t0) REVERT: r 398 MET cc_start: 0.8354 (mmp) cc_final: 0.8119 (mmm) REVERT: s 121 TRP cc_start: 0.8012 (t60) cc_final: 0.7523 (t60) REVERT: s 170 GLU cc_start: 0.7637 (tt0) cc_final: 0.7354 (tt0) REVERT: s 234 MET cc_start: 0.8652 (mmm) cc_final: 0.8286 (mmt) REVERT: v 48 ASP cc_start: 0.8171 (m-30) cc_final: 0.7848 (m-30) REVERT: v 76 ASN cc_start: 0.7922 (t0) cc_final: 0.7699 (p0) REVERT: v 105 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: w 120 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7204 (p0) REVERT: w 214 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8465 (tt) REVERT: w 353 TRP cc_start: 0.8793 (p-90) cc_final: 0.8571 (p-90) outliers start: 56 outliers final: 44 residues processed: 762 average time/residue: 0.2302 time to fit residues: 286.3761 Evaluate side-chains 766 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 715 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 43 SER Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 120 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 209 optimal weight: 0.8980 chunk 52 optimal weight: 0.0570 chunk 266 optimal weight: 5.9990 chunk 419 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 0.0980 chunk 371 optimal weight: 2.9990 chunk 434 optimal weight: 0.9980 chunk 235 optimal weight: 0.3980 chunk 287 optimal weight: 0.0980 chunk 222 optimal weight: 1.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 123 GLN r 43 ASN u 16 GLN w 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.104484 restraints weight = 53867.576| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.44 r_work: 0.3018 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 39630 Z= 0.103 Angle : 0.519 11.284 53568 Z= 0.259 Chirality : 0.038 0.201 5831 Planarity : 0.004 0.050 6553 Dihedral : 11.835 120.155 6161 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.21 % Allowed : 12.82 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 2.53 (0.13), residues: 4586 helix: 2.64 (0.09), residues: 2961 sheet: -0.23 (1.26), residues: 26 loop : -0.14 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG r 340 TYR 0.026 0.001 TYR w 129 PHE 0.029 0.001 PHE l 335 TRP 0.022 0.001 TRP w 353 HIS 0.007 0.001 HIS r 83 Details of bonding type rmsd covalent geometry : bond 0.00221 (39623) covalent geometry : angle 0.51901 (53556) SS BOND : bond 0.00293 ( 6) SS BOND : angle 1.29559 ( 12) hydrogen bonds : bond 0.03659 ( 2300) hydrogen bonds : angle 3.78220 ( 6705) Misc. bond : bond 0.00042 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 751 time to evaluate : 1.540 Fit side-chains REVERT: U 51 TYR cc_start: 0.8882 (m-80) cc_final: 0.8557 (m-80) REVERT: V 44 LYS cc_start: 0.7553 (mmtt) cc_final: 0.7237 (pttt) REVERT: V 106 ARG cc_start: 0.6359 (tpm170) cc_final: 0.4373 (mtt90) REVERT: W 121 MET cc_start: 0.8456 (tpp) cc_final: 0.8200 (tpp) REVERT: X 74 LEU cc_start: 0.8633 (pt) cc_final: 0.8283 (pt) REVERT: X 146 ASP cc_start: 0.7995 (m-30) cc_final: 0.7763 (m-30) REVERT: Z 61 VAL cc_start: 0.8672 (m) cc_final: 0.8234 (p) REVERT: a 127 ASP cc_start: 0.8748 (m-30) cc_final: 0.8078 (t0) REVERT: c 81 ARG cc_start: 0.8863 (mmt90) cc_final: 0.8643 (mmm-85) REVERT: c 148 GLU cc_start: 0.8404 (tp30) cc_final: 0.8194 (tp30) REVERT: i 187 MET cc_start: 0.8933 (mmm) cc_final: 0.8702 (mmm) REVERT: i 282 MET cc_start: 0.8586 (mtt) cc_final: 0.8370 (mtp) REVERT: k 26 LEU cc_start: 0.7689 (tp) cc_final: 0.7378 (tp) REVERT: k 82 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8571 (p) REVERT: l 186 MET cc_start: 0.9064 (ttm) cc_final: 0.8788 (ttp) REVERT: l 340 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8858 (m-80) REVERT: l 475 MET cc_start: 0.7645 (mtt) cc_final: 0.7325 (mmt) REVERT: l 484 LEU cc_start: 0.7990 (mt) cc_final: 0.7414 (mt) REVERT: m 1 MET cc_start: 0.2823 (tmm) cc_final: 0.2276 (tpt) REVERT: m 137 SER cc_start: 0.9096 (OUTLIER) cc_final: 0.8675 (t) REVERT: m 141 MET cc_start: 0.7889 (mmm) cc_final: 0.7623 (mmm) REVERT: m 173 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8248 (ttp80) REVERT: n 58 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7691 (ttpt) REVERT: o 31 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8779 (tttm) REVERT: r 398 MET cc_start: 0.8311 (mmp) cc_final: 0.8094 (mmm) REVERT: s 121 TRP cc_start: 0.7937 (t60) cc_final: 0.7524 (t60) REVERT: s 170 GLU cc_start: 0.7563 (tt0) cc_final: 0.7285 (tt0) REVERT: v 48 ASP cc_start: 0.8143 (m-30) cc_final: 0.7815 (m-30) REVERT: v 105 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: w 120 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7124 (p0) REVERT: w 214 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8438 (tt) REVERT: w 353 TRP cc_start: 0.8794 (p-90) cc_final: 0.8582 (p-90) outliers start: 49 outliers final: 36 residues processed: 777 average time/residue: 0.2318 time to fit residues: 294.7066 Evaluate side-chains 762 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 720 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 120 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 439 optimal weight: 0.0470 chunk 223 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 323 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN ** s 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104853 restraints weight = 54028.680| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.41 r_work: 0.3006 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.205 39630 Z= 0.126 Angle : 0.626 59.168 53568 Z= 0.338 Chirality : 0.039 0.449 5831 Planarity : 0.004 0.050 6553 Dihedral : 11.835 120.177 6161 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 1.24 % Allowed : 13.24 % Favored : 85.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.83 % 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: 2.52 (0.13), residues: 4586 helix: 2.63 (0.09), residues: 2961 sheet: -0.23 (1.26), residues: 26 loop : -0.15 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG r 340 TYR 0.024 0.001 TYR l 422 PHE 0.029 0.001 PHE l 335 TRP 0.020 0.001 TRP w 353 HIS 0.014 0.001 HIS s 250 Details of bonding type rmsd covalent geometry : bond 0.00289 (39623) covalent geometry : angle 0.62542 (53556) SS BOND : bond 0.00337 ( 6) SS BOND : angle 1.26607 ( 12) hydrogen bonds : bond 0.03698 ( 2300) hydrogen bonds : angle 3.78411 ( 6705) Misc. bond : bond 0.00027 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12025.07 seconds wall clock time: 205 minutes 39.06 seconds (12339.06 seconds total)