Starting phenix.real_space_refine on Fri Mar 6 02:51:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tr6_26081/03_2026/7tr6_26081_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tr6_26081/03_2026/7tr6_26081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tr6_26081/03_2026/7tr6_26081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tr6_26081/03_2026/7tr6_26081.map" model { file = "/net/cci-nas-00/data/ceres_data/7tr6_26081/03_2026/7tr6_26081_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tr6_26081/03_2026/7tr6_26081_neut.cif" } resolution = 3.4 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= 0.033 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 44 5.49 5 S 59 5.16 5 C 17422 2.51 5 N 4681 2.21 5 O 5243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 27449 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "E" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "I" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} 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: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2494 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2134 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "R" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 949 Classifications: {'RNA': 45} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 13, 'rna3p_pyr': 13} Link IDs: {'rna2p': 18, 'rna3p': 26} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.91, per 1000 atoms: 0.25 Number of scatterers: 27449 At special positions: 0 Unit cell: (112.205, 129.086, 204.552, 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 59 16.00 P 44 15.00 O 5243 8.00 N 4681 7.00 C 17422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6270 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 41 sheets defined 38.3% alpha, 11.9% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 21 through 28 removed outlier: 3.541A pdb=" N SER C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 71 removed outlier: 3.666A pdb=" N ASP C 60 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 3.589A pdb=" N SER C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 103 " --> pdb=" O TYR C 99 " (cutoff:3.500A) Proline residue: C 104 - end of helix removed outlier: 3.591A pdb=" N LEU C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 193 through 204 removed outlier: 3.634A pdb=" N ASP C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.755A pdb=" N LEU C 218 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE C 219 " --> pdb=" O ASP C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 219' Processing helix chain 'C' and resid 220 through 231 removed outlier: 4.280A pdb=" N LEU C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.643A pdb=" N ILE C 286 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS C 287 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 288 " --> pdb=" O HIS C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 310 Processing helix chain 'C' and resid 311 through 326 removed outlier: 4.342A pdb=" N PHE C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.686A pdb=" N VAL C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 removed outlier: 3.758A pdb=" N TYR D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU D 15 " --> pdb=" O TYR D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 33 removed outlier: 4.495A pdb=" N VAL D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 removed outlier: 3.889A pdb=" N LEU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 62 removed outlier: 4.104A pdb=" N SER D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.741A pdb=" N GLU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 100 removed outlier: 3.986A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU D 93 " --> pdb=" O ASP D 89 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER D 96 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.777A pdb=" N ASN E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 16 No H-bonds generated for 'chain 'E' and resid 14 through 16' Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.924A pdb=" N VAL E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.779A pdb=" N LEU E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 59 removed outlier: 4.225A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 70 through 83 Processing helix chain 'E' and resid 86 through 100 removed outlier: 4.172A pdb=" N LYS E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TRP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 14 removed outlier: 3.638A pdb=" N TYR F 14 " --> pdb=" O ARG F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 removed outlier: 4.186A pdb=" N VAL F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 50 removed outlier: 3.940A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 61 removed outlier: 4.122A pdb=" N GLU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 removed outlier: 3.753A pdb=" N ILE F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 100 removed outlier: 3.529A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 93 " --> pdb=" O ASP F 89 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'G' and resid 5 through 14 removed outlier: 3.639A pdb=" N TYR G 11 " --> pdb=" O ASN G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.815A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 50 removed outlier: 3.902A pdb=" N LEU G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 61 removed outlier: 3.953A pdb=" N LYS G 56 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS G 57 " --> pdb=" O LYS G 53 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.894A pdb=" N ILE G 74 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU G 75 " --> pdb=" O PRO G 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 98 removed outlier: 3.708A pdb=" N ALA G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 14 Processing helix chain 'H' and resid 24 through 33 removed outlier: 4.321A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 Processing helix chain 'H' and resid 50 through 59 removed outlier: 4.331A pdb=" N GLU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.673A pdb=" N LEU H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 100 removed outlier: 3.794A pdb=" N LEU H 93 " --> pdb=" O ASP H 89 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 70 removed outlier: 3.714A pdb=" N LEU I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS I 68 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.757A pdb=" N LEU I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG I 82 " --> pdb=" O GLU I 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 77 through 82' Processing helix chain 'I' and resid 107 through 115 removed outlier: 3.531A pdb=" N ILE I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 122 Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'I' and resid 227 through 242 removed outlier: 3.608A pdb=" N LEU I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 300 Processing helix chain 'I' and resid 324 through 333 Processing helix chain 'J' and resid 51 through 69 removed outlier: 3.738A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 75 removed outlier: 4.564A pdb=" N VAL J 74 " --> pdb=" O PRO J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 3.661A pdb=" N ARG J 82 " --> pdb=" O GLU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 115 removed outlier: 3.556A pdb=" N ILE J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 121 Processing helix chain 'J' and resid 144 through 152 removed outlier: 3.582A pdb=" N GLU J 152 " --> pdb=" O ILE J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 205 Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 242 through 243 No H-bonds generated for 'chain 'J' and resid 242 through 243' Processing helix chain 'J' and resid 244 through 248 removed outlier: 3.544A pdb=" N SER J 247 " --> pdb=" O PRO J 244 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY J 248 " --> pdb=" O MET J 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 244 through 248' Processing helix chain 'J' and resid 285 through 300 Processing helix chain 'J' and resid 324 through 335 removed outlier: 3.750A pdb=" N MET J 335 " --> pdb=" O ASN J 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 69 removed outlier: 3.514A pdb=" N LEU K 55 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 115 through 121 Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 242 through 247 Processing helix chain 'K' and resid 286 through 301 removed outlier: 3.617A pdb=" N ALA K 297 " --> pdb=" O ILE K 293 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY K 301 " --> pdb=" O ALA K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 335 removed outlier: 3.591A pdb=" N MET K 335 " --> pdb=" O ASN K 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 69 removed outlier: 3.654A pdb=" N LYS L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 81 Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 115 through 122 removed outlier: 3.593A pdb=" N ASP L 119 " --> pdb=" O LEU L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 152 removed outlier: 3.560A pdb=" N GLU L 152 " --> pdb=" O ILE L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 241 through 246 removed outlier: 3.942A pdb=" N MET L 245 " --> pdb=" O ALA L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 299 removed outlier: 3.875A pdb=" N ALA L 289 " --> pdb=" O ASP L 285 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA L 297 " --> pdb=" O ILE L 293 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA L 299 " --> pdb=" O LYS L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 335 removed outlier: 3.596A pdb=" N LYS L 334 " --> pdb=" O ALA L 330 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET L 335 " --> pdb=" O ASN L 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 24 removed outlier: 3.513A pdb=" N GLY M 23 " --> pdb=" O GLY M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 69 removed outlier: 3.514A pdb=" N LEU M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 removed outlier: 4.072A pdb=" N ARG M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 115 removed outlier: 3.858A pdb=" N ILE M 111 " --> pdb=" O ASP M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 122 Processing helix chain 'M' and resid 144 through 151 removed outlier: 3.507A pdb=" N GLU M 150 " --> pdb=" O ASP M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 285 through 295 removed outlier: 3.737A pdb=" N ILE M 293 " --> pdb=" O ALA M 289 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 300 Processing helix chain 'M' and resid 325 through 335 removed outlier: 4.129A pdb=" N MET M 335 " --> pdb=" O ASN M 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 69 removed outlier: 3.534A pdb=" N LEU N 55 " --> pdb=" O THR N 51 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 3.754A pdb=" N ARG N 82 " --> pdb=" O GLU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 115 removed outlier: 3.607A pdb=" N ILE N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 122 removed outlier: 3.957A pdb=" N VAL N 120 " --> pdb=" O ALA N 116 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N HIS N 121 " --> pdb=" O ASP N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 152 removed outlier: 3.621A pdb=" N GLU N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU N 152 " --> pdb=" O ILE N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 155 No H-bonds generated for 'chain 'N' and resid 153 through 155' Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 285 through 301 removed outlier: 3.545A pdb=" N ALA N 289 " --> pdb=" O ASP N 285 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER N 292 " --> pdb=" O GLU N 288 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA N 297 " --> pdb=" O ILE N 293 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY N 301 " --> pdb=" O ALA N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 336 Processing helix chain 'O' and resid 51 through 69 removed outlier: 3.576A pdb=" N LEU O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR O 69 " --> pdb=" O ASP O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 Processing helix chain 'O' and resid 107 through 113 removed outlier: 3.525A pdb=" N ILE O 111 " --> pdb=" O ASP O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 121 Processing helix chain 'O' and resid 144 through 149 Processing helix chain 'O' and resid 202 through 205 removed outlier: 3.635A pdb=" N VAL O 205 " --> pdb=" O LEU O 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 202 through 205' Processing helix chain 'O' and resid 227 through 241 Processing helix chain 'O' and resid 242 through 247 removed outlier: 3.792A pdb=" N LEU O 246 " --> pdb=" O ILE O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 285 through 298 Processing helix chain 'O' and resid 324 through 335 removed outlier: 3.738A pdb=" N MET O 335 " --> pdb=" O ASN O 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 46 Processing helix chain 'P' and resid 54 through 70 Processing helix chain 'P' and resid 129 through 141 removed outlier: 3.926A pdb=" N ASN P 134 " --> pdb=" O GLN P 130 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 182 removed outlier: 4.005A pdb=" N SER P 181 " --> pdb=" O GLU P 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'C' and resid 123 through 125 removed outlier: 3.621A pdb=" N VAL C 152 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 170 through 173 Processing sheet with id=AA4, first strand: chain 'I' and resid 2 through 10 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 2 through 10 current: chain 'I' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 193 through 201 current: chain 'I' and resid 305 through 309 removed outlier: 7.029A pdb=" N VAL I 306 " --> pdb=" O THR I 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'I' and resid 26 through 27 removed outlier: 3.535A pdb=" N MET I 183 " --> pdb=" O ARG I 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 32 through 37 Processing sheet with id=AA7, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AA8, first strand: chain 'I' and resid 123 through 125 removed outlier: 7.249A pdb=" N PHE I 123 " --> pdb=" O ARG I 131 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG I 131 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA I 125 " --> pdb=" O GLY I 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 3 through 14 current: chain 'J' and resid 184 through 200 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 184 through 200 current: chain 'J' and resid 305 through 309 Processing sheet with id=AB1, first strand: chain 'J' and resid 31 through 36 Processing sheet with id=AB2, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AB3, first strand: chain 'J' and resid 123 through 124 Processing sheet with id=AB4, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 184 through 201 current: chain 'K' and resid 305 through 309 Processing sheet with id=AB5, first strand: chain 'K' and resid 31 through 36 Processing sheet with id=AB6, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AB7, first strand: chain 'K' and resid 123 through 124 Processing sheet with id=AB8, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 186 through 196 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 186 through 196 current: chain 'L' and resid 305 through 309 Processing sheet with id=AB9, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AC1, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AC2, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AC3, first strand: chain 'M' and resid 2 through 10 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 10 current: chain 'M' and resid 193 through 196 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 193 through 196 current: chain 'M' and resid 306 through 309 Processing sheet with id=AC4, first strand: chain 'M' and resid 26 through 27 Processing sheet with id=AC5, first strand: chain 'M' and resid 31 through 36 Processing sheet with id=AC6, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AC7, first strand: chain 'M' and resid 123 through 124 removed outlier: 3.539A pdb=" N PHE M 123 " --> pdb=" O ARG M 132 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 213 through 215 Processing sheet with id=AC9, first strand: chain 'N' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 2 through 12 current: chain 'N' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 193 through 201 current: chain 'N' and resid 305 through 309 Processing sheet with id=AD1, first strand: chain 'N' and resid 26 through 27 Processing sheet with id=AD2, first strand: chain 'N' and resid 31 through 36 Processing sheet with id=AD3, first strand: chain 'N' and resid 94 through 96 Processing sheet with id=AD4, first strand: chain 'N' and resid 123 through 125 Processing sheet with id=AD5, first strand: chain 'O' and resid 136 through 138 removed outlier: 3.566A pdb=" N GLU O 265 " --> pdb=" O ARG O 8 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG O 10 " --> pdb=" O VAL O 263 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL O 263 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU O 266 " --> pdb=" O TYR O 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 32 through 35 removed outlier: 3.511A pdb=" N THR O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL O 47 " --> pdb=" O THR O 32 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 94 through 96 Processing sheet with id=AD8, first strand: chain 'O' and resid 123 through 125 Processing sheet with id=AD9, first strand: chain 'P' and resid 77 through 80 removed outlier: 4.407A pdb=" N SER P 77 " --> pdb=" O ALA P 122 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA P 122 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP P 157 " --> pdb=" O CYS P 7 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 12 through 13 removed outlier: 3.501A pdb=" N THR P 114 " --> pdb=" O PHE P 13 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 90 through 91 Processing sheet with id=AE3, first strand: chain 'P' and resid 168 through 169 Processing sheet with id=AE4, first strand: chain 'P' and resid 174 through 175 removed outlier: 3.540A pdb=" N ALA P 174 " --> pdb=" O TYR P 218 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 243 through 246 867 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 4.80 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8108 1.33 - 1.45: 4387 1.45 - 1.57: 15399 1.57 - 1.69: 88 1.69 - 1.81: 106 Bond restraints: 28088 Sorted by residual: bond pdb=" CA VAL I 279 " pdb=" CB VAL I 279 " ideal model delta sigma weight residual 1.553 1.540 0.013 7.40e-03 1.83e+04 3.08e+00 bond pdb=" N TYR C 211 " pdb=" CA TYR C 211 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.33e+00 bond pdb=" CA LEU C 207 " pdb=" CB LEU C 207 " ideal model delta sigma weight residual 1.522 1.532 -0.010 7.00e-03 2.04e+04 2.06e+00 bond pdb=" C3' A R 1 " pdb=" O3' A R 1 " ideal model delta sigma weight residual 1.415 1.438 -0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" CB GLU I 284 " pdb=" CG GLU I 284 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 28083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 37698 2.00 - 4.00: 498 4.00 - 6.00: 61 6.00 - 8.01: 12 8.01 - 10.01: 2 Bond angle restraints: 38271 Sorted by residual: angle pdb=" C THR N 38 " pdb=" CA THR N 38 " pdb=" CB THR N 38 " ideal model delta sigma weight residual 116.54 110.07 6.47 1.15e+00 7.56e-01 3.17e+01 angle pdb=" CA THR N 38 " pdb=" C THR N 38 " pdb=" N GLU N 39 " ideal model delta sigma weight residual 119.52 116.78 2.74 7.90e-01 1.60e+00 1.20e+01 angle pdb=" CA GLU P 164 " pdb=" CB GLU P 164 " pdb=" CG GLU P 164 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 angle pdb=" C TYR C 211 " pdb=" CA TYR C 211 " pdb=" CB TYR C 211 " ideal model delta sigma weight residual 110.42 116.43 -6.01 1.99e+00 2.53e-01 9.11e+00 angle pdb=" CA LEU P 142 " pdb=" CB LEU P 142 " pdb=" CG LEU P 142 " ideal model delta sigma weight residual 116.30 126.31 -10.01 3.50e+00 8.16e-02 8.17e+00 ... (remaining 38266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 16589 35.41 - 70.81: 353 70.81 - 106.22: 34 106.22 - 141.63: 2 141.63 - 177.03: 5 Dihedral angle restraints: 16983 sinusoidal: 7220 harmonic: 9763 Sorted by residual: dihedral pdb=" O4' U R 3 " pdb=" C1' U R 3 " pdb=" N1 U R 3 " pdb=" C2 U R 3 " ideal model delta sinusoidal sigma weight residual 200.00 36.95 163.05 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' U R 14 " pdb=" C1' U R 14 " pdb=" N1 U R 14 " pdb=" C2 U R 14 " ideal model delta sinusoidal sigma weight residual 200.00 45.94 154.06 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' C R 40 " pdb=" C1' C R 40 " pdb=" N1 C R 40 " pdb=" C2 C R 40 " ideal model delta sinusoidal sigma weight residual 232.00 54.97 177.03 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2991 0.038 - 0.076: 991 0.076 - 0.113: 328 0.113 - 0.151: 73 0.151 - 0.189: 6 Chirality restraints: 4389 Sorted by residual: chirality pdb=" C3' A R 1 " pdb=" C4' A R 1 " pdb=" O3' A R 1 " pdb=" C2' A R 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.31 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" C3' C R 18 " pdb=" C4' C R 18 " pdb=" O3' C R 18 " pdb=" C2' C R 18 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" C1' U R 14 " pdb=" O4' U R 14 " pdb=" C2' U R 14 " pdb=" N1 U R 14 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 4386 not shown) Planarity restraints: 4745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS P 162 " -0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO P 163 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO P 163 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO P 163 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 103 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO C 104 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 243 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO I 244 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 244 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 244 " 0.027 5.00e-02 4.00e+02 ... (remaining 4742 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 718 2.69 - 3.24: 28303 3.24 - 3.79: 44353 3.79 - 4.35: 58609 4.35 - 4.90: 95259 Nonbonded interactions: 227242 Sorted by model distance: nonbonded pdb=" OE1 GLU I 265 " pdb=" OH TYR I 286 " model vdw 2.136 3.040 nonbonded pdb=" NH1 ARG P 110 " pdb=" OE1 GLU P 112 " model vdw 2.148 3.120 nonbonded pdb=" OD1 ASP K 65 " pdb=" OH TYR K 83 " model vdw 2.164 3.040 nonbonded pdb=" O ASN J 253 " pdb=" OG SER J 257 " model vdw 2.167 3.040 nonbonded pdb=" O2' A R 1 " pdb=" OP2 U R 2 " model vdw 2.188 3.040 ... (remaining 227237 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 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and resid 3 through 109) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 164 or resid 180 th \ rough 335)) selection = (chain 'J' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 164 or resid 180 through 335)) selection = (chain 'K' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'L' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'M' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'N' and resid 1 through 335) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.830 Find NCS groups from input model: 0.530 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 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 : 0.003 0.043 28093 Z= 0.127 Angle : 0.574 10.007 38281 Z= 0.303 Chirality : 0.043 0.189 4389 Planarity : 0.004 0.093 4745 Dihedral : 15.203 177.034 10698 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.61 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.15), residues: 3341 helix: 0.52 (0.17), residues: 1053 sheet: -0.05 (0.23), residues: 570 loop : -1.38 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 131 TYR 0.018 0.001 TYR C 157 PHE 0.013 0.001 PHE C 54 TRP 0.022 0.002 TRP H 105 HIS 0.006 0.001 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00275 (28088) covalent geometry : angle 0.57425 (38271) SS BOND : bond 0.00032 ( 5) SS BOND : angle 0.64967 ( 10) hydrogen bonds : bond 0.15472 ( 867) hydrogen bonds : angle 5.95984 ( 2478) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 741 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 VAL cc_start: 0.0153 (t) cc_final: -0.0552 (t) REVERT: C 191 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6343 (pt0) REVERT: C 200 LEU cc_start: 0.6944 (mm) cc_final: 0.6716 (mp) REVERT: C 226 LEU cc_start: 0.7453 (tp) cc_final: 0.7235 (pp) REVERT: C 243 PHE cc_start: 0.2614 (m-80) cc_final: 0.2256 (m-80) REVERT: C 248 TYR cc_start: 0.4395 (p90) cc_final: 0.4094 (p90) REVERT: C 262 PHE cc_start: 0.5921 (t80) cc_final: 0.5610 (t80) REVERT: C 271 MET cc_start: 0.0299 (ttt) cc_final: 0.0072 (tmm) REVERT: C 282 PHE cc_start: 0.2561 (t80) cc_final: 0.2319 (t80) REVERT: D 20 PHE cc_start: 0.8309 (m-80) cc_final: 0.7944 (m-10) REVERT: D 99 LEU cc_start: 0.7488 (mt) cc_final: 0.7183 (mt) REVERT: F 10 ARG cc_start: 0.7124 (tpt-90) cc_final: 0.6901 (tpt90) REVERT: G 25 TYR cc_start: 0.6877 (m-80) cc_final: 0.6443 (m-10) REVERT: H 75 GLU cc_start: 0.6726 (tt0) cc_final: 0.6121 (mm-30) REVERT: I 108 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7247 (tt0) REVERT: I 288 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7575 (mp0) REVERT: I 293 ILE cc_start: 0.4457 (tp) cc_final: 0.4097 (mt) REVERT: J 202 LEU cc_start: 0.4805 (mt) cc_final: 0.4538 (mt) REVERT: J 223 ASN cc_start: 0.5585 (t0) cc_final: 0.5295 (m-40) REVERT: K 1 MET cc_start: 0.4863 (tmm) cc_final: 0.4616 (tmm) REVERT: K 96 THR cc_start: 0.7328 (m) cc_final: 0.6436 (m) REVERT: K 183 MET cc_start: 0.5945 (pmm) cc_final: 0.5515 (pmm) REVERT: K 293 ILE cc_start: 0.8994 (tt) cc_final: 0.8708 (tp) REVERT: L 96 THR cc_start: 0.7761 (t) cc_final: 0.7165 (p) REVERT: L 214 LYS cc_start: 0.8199 (tppt) cc_final: 0.6861 (ptpt) REVERT: M 96 THR cc_start: 0.8650 (m) cc_final: 0.8324 (p) REVERT: O 10 ARG cc_start: 0.6618 (ttm170) cc_final: 0.4806 (tmm160) REVERT: O 64 VAL cc_start: 0.6918 (t) cc_final: 0.6582 (m) REVERT: O 105 LEU cc_start: 0.6668 (mp) cc_final: 0.6374 (mt) REVERT: P 1 MET cc_start: 0.4417 (mmt) cc_final: 0.4205 (mpp) REVERT: P 93 ARG cc_start: 0.4184 (mmp-170) cc_final: 0.3440 (mtt90) REVERT: P 98 GLU cc_start: 0.1650 (pm20) cc_final: -0.0183 (tm-30) REVERT: P 242 LYS cc_start: 0.5200 (tptp) cc_final: 0.4223 (pttp) outliers start: 0 outliers final: 0 residues processed: 741 average time/residue: 0.2090 time to fit residues: 237.1776 Evaluate side-chains 361 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS I 182 GLN I 223 ASN K 17 ASN K 53 ASN K 162 HIS L 310 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 GLN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.153895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.118088 restraints weight = 63551.484| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 3.40 r_work: 0.3644 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 28093 Z= 0.223 Angle : 0.745 17.864 38281 Z= 0.380 Chirality : 0.049 0.266 4389 Planarity : 0.006 0.114 4745 Dihedral : 12.233 176.219 4355 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.97 % Favored : 93.00 % Rotamer: Outliers : 2.70 % Allowed : 12.82 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.15), residues: 3341 helix: 0.13 (0.16), residues: 1160 sheet: -0.02 (0.23), residues: 538 loop : -1.63 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 10 TYR 0.026 0.002 TYR E 11 PHE 0.028 0.002 PHE C 288 TRP 0.019 0.002 TRP E 105 HIS 0.009 0.002 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00471 (28088) covalent geometry : angle 0.74539 (38271) SS BOND : bond 0.00098 ( 5) SS BOND : angle 0.59840 ( 10) hydrogen bonds : bond 0.04091 ( 867) hydrogen bonds : angle 4.82656 ( 2478) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 417 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 SER cc_start: 0.5672 (m) cc_final: 0.5042 (p) REVERT: C 111 MET cc_start: 0.0132 (mmm) cc_final: -0.0521 (ptt) REVERT: C 191 GLU cc_start: 0.6421 (mm-30) cc_final: 0.6017 (mt-10) REVERT: C 262 PHE cc_start: 0.5981 (t80) cc_final: 0.5650 (t80) REVERT: C 283 TYR cc_start: 0.5672 (t80) cc_final: 0.5054 (p90) REVERT: D 5 ILE cc_start: 0.3033 (OUTLIER) cc_final: 0.2802 (tp) REVERT: D 46 LYS cc_start: 0.8322 (mmmm) cc_final: 0.8003 (mttp) REVERT: E 78 GLU cc_start: 0.6549 (tp30) cc_final: 0.5529 (tt0) REVERT: H 72 GLU cc_start: 0.8522 (tp30) cc_final: 0.7848 (mp0) REVERT: H 75 GLU cc_start: 0.6349 (tt0) cc_final: 0.6060 (mm-30) REVERT: H 79 GLU cc_start: 0.8371 (pm20) cc_final: 0.8169 (pm20) REVERT: I 58 TRP cc_start: 0.5955 (m100) cc_final: 0.5688 (m100) REVERT: I 108 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7584 (tt0) REVERT: I 183 MET cc_start: 0.4326 (ptm) cc_final: 0.3901 (ptp) REVERT: I 288 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7749 (mp0) REVERT: I 293 ILE cc_start: 0.3670 (tp) cc_final: 0.3353 (mt) REVERT: J 316 ASP cc_start: 0.8428 (m-30) cc_final: 0.8084 (m-30) REVERT: K 293 ILE cc_start: 0.9046 (tt) cc_final: 0.8649 (tt) REVERT: K 332 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8366 (mt) REVERT: L 285 ASP cc_start: 0.7841 (t0) cc_final: 0.7630 (t0) REVERT: L 310 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7829 (p0) REVERT: M 230 GLU cc_start: 0.7283 (tp30) cc_final: 0.6914 (tt0) REVERT: M 264 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7548 (mm-30) REVERT: N 226 ILE cc_start: 0.7622 (pt) cc_final: 0.7342 (pt) REVERT: O 10 ARG cc_start: 0.7137 (ttm170) cc_final: 0.5237 (tmm160) REVERT: O 67 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6680 (t80) REVERT: O 82 ARG cc_start: 0.6874 (ptp90) cc_final: 0.5581 (mmt180) REVERT: O 104 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: O 211 LEU cc_start: 0.7112 (tp) cc_final: 0.6742 (mp) REVERT: P 98 GLU cc_start: 0.1991 (pm20) cc_final: -0.0401 (tm-30) REVERT: P 216 ILE cc_start: 0.6304 (mp) cc_final: 0.6049 (tt) REVERT: P 242 LYS cc_start: 0.5486 (tptp) cc_final: 0.4510 (pttp) outliers start: 76 outliers final: 44 residues processed: 477 average time/residue: 0.1965 time to fit residues: 148.0802 Evaluate side-chains 360 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 311 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 321 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 333 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 286 TYR Chi-restraints excluded: chain L residue 310 ASN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 198 ILE Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain O residue 226 ILE Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain P residue 156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 221 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN I 17 ASN I 223 ASN K 162 HIS L 12 ASN L 53 ASN L 229 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN N 25 ASN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.150478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.111544 restraints weight = 63398.336| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.21 r_work: 0.3584 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28093 Z= 0.156 Angle : 0.636 10.681 38281 Z= 0.324 Chirality : 0.045 0.258 4389 Planarity : 0.005 0.086 4745 Dihedral : 12.196 176.213 4355 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.76 % Favored : 93.18 % Rotamer: Outliers : 3.02 % Allowed : 16.65 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.05 (0.15), residues: 3341 helix: 0.16 (0.16), residues: 1184 sheet: -0.13 (0.23), residues: 538 loop : -1.55 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 10 TYR 0.019 0.001 TYR J 72 PHE 0.024 0.002 PHE O 196 TRP 0.028 0.002 TRP G 105 HIS 0.006 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00359 (28088) covalent geometry : angle 0.63546 (38271) SS BOND : bond 0.00080 ( 5) SS BOND : angle 0.85632 ( 10) hydrogen bonds : bond 0.03542 ( 867) hydrogen bonds : angle 4.57869 ( 2478) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 327 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 SER cc_start: 0.5818 (m) cc_final: 0.5579 (p) REVERT: C 262 PHE cc_start: 0.6134 (t80) cc_final: 0.5662 (t80) REVERT: C 283 TYR cc_start: 0.5687 (t80) cc_final: 0.5071 (p90) REVERT: D 5 ILE cc_start: 0.3240 (OUTLIER) cc_final: 0.3018 (tp) REVERT: E 29 ASP cc_start: 0.8075 (m-30) cc_final: 0.7618 (p0) REVERT: H 75 GLU cc_start: 0.6624 (tt0) cc_final: 0.5992 (mm-30) REVERT: H 79 GLU cc_start: 0.8287 (pm20) cc_final: 0.8030 (mm-30) REVERT: I 58 TRP cc_start: 0.6470 (m100) cc_final: 0.5775 (m100) REVERT: I 108 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7772 (tt0) REVERT: I 183 MET cc_start: 0.4598 (ptm) cc_final: 0.4254 (ptp) REVERT: I 253 ASN cc_start: 0.6854 (t0) cc_final: 0.6472 (t0) REVERT: I 265 GLU cc_start: 0.4267 (tt0) cc_final: 0.3842 (tt0) REVERT: I 276 PRO cc_start: 0.4094 (Cg_endo) cc_final: 0.3668 (Cg_exo) REVERT: I 288 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7661 (mp0) REVERT: I 293 ILE cc_start: 0.3844 (tp) cc_final: 0.3469 (mt) REVERT: I 323 SER cc_start: 0.6496 (m) cc_final: 0.6274 (m) REVERT: J 2 TYR cc_start: 0.8019 (m-80) cc_final: 0.7684 (m-80) REVERT: J 53 ASN cc_start: 0.7869 (t0) cc_final: 0.7357 (t0) REVERT: J 316 ASP cc_start: 0.8329 (m-30) cc_final: 0.7958 (p0) REVERT: K 111 ILE cc_start: 0.9162 (mt) cc_final: 0.8919 (mp) REVERT: M 326 GLU cc_start: 0.7276 (pm20) cc_final: 0.7047 (pm20) REVERT: O 10 ARG cc_start: 0.7393 (ttm170) cc_final: 0.5781 (ptt90) REVERT: O 30 THR cc_start: 0.6458 (p) cc_final: 0.6164 (t) REVERT: O 67 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.6641 (t80) REVERT: O 82 ARG cc_start: 0.7051 (ptp90) cc_final: 0.5581 (mmt180) REVERT: O 245 MET cc_start: 0.6728 (mtp) cc_final: 0.6179 (ttm) REVERT: P 98 GLU cc_start: 0.1326 (pm20) cc_final: -0.0509 (tm-30) REVERT: P 242 LYS cc_start: 0.5578 (tptp) cc_final: 0.4595 (pttp) outliers start: 85 outliers final: 41 residues processed: 394 average time/residue: 0.1838 time to fit residues: 117.8925 Evaluate side-chains 311 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 268 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 237 SER Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 198 ILE Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 226 ILE Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain P residue 44 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 203 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 27 optimal weight: 40.0000 chunk 118 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN I 17 ASN J 162 HIS K 17 ASN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN N 53 ASN ** O 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.137878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097480 restraints weight = 62388.821| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.47 r_work: 0.3284 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.7505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 28093 Z= 0.311 Angle : 0.867 18.132 38281 Z= 0.446 Chirality : 0.053 0.263 4389 Planarity : 0.007 0.075 4745 Dihedral : 12.431 177.306 4355 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.44 % Favored : 91.50 % Rotamer: Outliers : 4.97 % Allowed : 18.53 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.73 (0.14), residues: 3341 helix: -0.50 (0.15), residues: 1192 sheet: -0.49 (0.22), residues: 558 loop : -1.89 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 110 TYR 0.045 0.003 TYR H 14 PHE 0.035 0.003 PHE O 88 TRP 0.060 0.003 TRP G 105 HIS 0.016 0.003 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00729 (28088) covalent geometry : angle 0.86676 (38271) SS BOND : bond 0.00252 ( 5) SS BOND : angle 0.81878 ( 10) hydrogen bonds : bond 0.04268 ( 867) hydrogen bonds : angle 5.05175 ( 2478) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 322 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 SER cc_start: 0.5610 (m) cc_final: 0.4906 (p) REVERT: C 111 MET cc_start: -0.0073 (mmm) cc_final: -0.0879 (ptt) REVERT: C 138 MET cc_start: -0.2993 (OUTLIER) cc_final: -0.3749 (tpp) REVERT: C 262 PHE cc_start: 0.6501 (t80) cc_final: 0.5724 (t80) REVERT: C 271 MET cc_start: -0.1002 (OUTLIER) cc_final: -0.1379 (mmm) REVERT: D 105 TRP cc_start: 0.5988 (m100) cc_final: 0.5542 (m100) REVERT: H 45 TYR cc_start: 0.3390 (OUTLIER) cc_final: 0.2495 (m-10) REVERT: H 72 GLU cc_start: 0.8614 (tp30) cc_final: 0.8251 (tm-30) REVERT: I 1 MET cc_start: 0.6439 (mmm) cc_final: 0.6191 (mmt) REVERT: I 19 GLN cc_start: 0.8443 (mp10) cc_final: 0.8175 (mp10) REVERT: I 149 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6868 (mmtt) REVERT: I 183 MET cc_start: 0.5157 (ptm) cc_final: 0.4710 (ptp) REVERT: I 230 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5906 (pp20) REVERT: I 253 ASN cc_start: 0.8508 (t0) cc_final: 0.7874 (t0) REVERT: I 257 SER cc_start: 0.7995 (m) cc_final: 0.6713 (m) REVERT: I 276 PRO cc_start: 0.4547 (Cg_endo) cc_final: 0.4203 (Cg_exo) REVERT: I 293 ILE cc_start: 0.4667 (tp) cc_final: 0.4320 (mt) REVERT: I 294 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7822 (pt) REVERT: K 202 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8626 (pp) REVERT: L 81 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8968 (mt) REVERT: L 217 GLU cc_start: 0.8078 (tp30) cc_final: 0.7417 (pt0) REVERT: N 1 MET cc_start: 0.8254 (ttm) cc_final: 0.7583 (ttm) REVERT: N 119 ASP cc_start: 0.7663 (t0) cc_final: 0.7360 (t0) REVERT: N 183 MET cc_start: 0.8068 (ppp) cc_final: 0.6755 (ppp) REVERT: O 1 MET cc_start: 0.7536 (tpp) cc_final: 0.7184 (tpt) REVERT: O 67 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7754 (t80) REVERT: O 245 MET cc_start: 0.7193 (mtp) cc_final: 0.6892 (ttm) REVERT: O 288 GLU cc_start: 0.8012 (tp30) cc_final: 0.7440 (tm-30) REVERT: O 304 ILE cc_start: 0.8598 (mp) cc_final: 0.8311 (mt) REVERT: P 98 GLU cc_start: 0.1332 (pm20) cc_final: 0.1006 (pm20) REVERT: P 167 LYS cc_start: 0.6184 (mptt) cc_final: 0.5874 (mttt) REVERT: P 242 LYS cc_start: 0.5420 (tptp) cc_final: 0.4311 (pttm) outliers start: 140 outliers final: 69 residues processed: 439 average time/residue: 0.1830 time to fit residues: 130.4597 Evaluate side-chains 330 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 253 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 303 ASN Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain P residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 204 optimal weight: 3.9990 chunk 328 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 279 optimal weight: 0.0270 chunk 282 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 250 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 259 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 HIS ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN I 53 ASN J 310 ASN L 182 GLN N 209 GLN O 14 HIS O 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.141578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103487 restraints weight = 61651.701| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.51 r_work: 0.3377 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.7582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28093 Z= 0.126 Angle : 0.648 13.671 38281 Z= 0.328 Chirality : 0.045 0.270 4389 Planarity : 0.005 0.064 4745 Dihedral : 12.239 178.392 4355 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 2.91 % Allowed : 21.62 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.14), residues: 3341 helix: -0.00 (0.15), residues: 1192 sheet: -0.35 (0.22), residues: 565 loop : -1.78 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 291 TYR 0.019 0.001 TYR G 14 PHE 0.019 0.001 PHE J 261 TRP 0.020 0.001 TRP H 105 HIS 0.004 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00276 (28088) covalent geometry : angle 0.64709 (38271) SS BOND : bond 0.00369 ( 5) SS BOND : angle 1.77003 ( 10) hydrogen bonds : bond 0.03091 ( 867) hydrogen bonds : angle 4.53728 ( 2478) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 296 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 SER cc_start: 0.5693 (m) cc_final: 0.5074 (p) REVERT: C 111 MET cc_start: 0.0026 (mmm) cc_final: -0.0750 (ptt) REVERT: C 262 PHE cc_start: 0.6447 (t80) cc_final: 0.5833 (t80) REVERT: D 37 GLN cc_start: 0.5964 (OUTLIER) cc_final: 0.5321 (tp40) REVERT: D 105 TRP cc_start: 0.6038 (m100) cc_final: 0.5426 (m100) REVERT: E 16 VAL cc_start: 0.8380 (t) cc_final: 0.7983 (m) REVERT: E 39 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: H 57 LYS cc_start: 0.7117 (tptp) cc_final: 0.6819 (tttm) REVERT: I 16 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7045 (mt) REVERT: I 28 GLU cc_start: 0.7524 (tt0) cc_final: 0.7072 (tm-30) REVERT: I 149 LYS cc_start: 0.6943 (mmtt) cc_final: 0.6716 (mmtt) REVERT: I 183 MET cc_start: 0.4976 (ptm) cc_final: 0.4506 (ptp) REVERT: I 213 VAL cc_start: 0.6371 (m) cc_final: 0.6058 (p) REVERT: I 230 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6069 (pp20) REVERT: I 253 ASN cc_start: 0.8469 (t0) cc_final: 0.8213 (t0) REVERT: I 293 ILE cc_start: 0.4438 (tp) cc_final: 0.4083 (mt) REVERT: J 316 ASP cc_start: 0.8377 (m-30) cc_final: 0.7929 (p0) REVERT: K 77 THR cc_start: 0.8767 (m) cc_final: 0.8527 (p) REVERT: K 104 GLN cc_start: 0.8206 (pm20) cc_final: 0.7856 (tp40) REVERT: K 202 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8523 (pp) REVERT: K 219 GLN cc_start: 0.7117 (pm20) cc_final: 0.6849 (pm20) REVERT: K 293 ILE cc_start: 0.9447 (tt) cc_final: 0.9141 (tt) REVERT: L 1 MET cc_start: 0.6978 (ttm) cc_final: 0.6726 (ttt) REVERT: L 183 MET cc_start: 0.6985 (pmm) cc_final: 0.6295 (ptt) REVERT: L 217 GLU cc_start: 0.8125 (tp30) cc_final: 0.7657 (pt0) REVERT: N 119 ASP cc_start: 0.7300 (t0) cc_final: 0.7033 (t0) REVERT: N 183 MET cc_start: 0.7952 (ppp) cc_final: 0.6808 (ppp) REVERT: N 219 GLN cc_start: 0.7388 (mt0) cc_final: 0.7063 (mp10) REVERT: O 1 MET cc_start: 0.7180 (tpp) cc_final: 0.6684 (tpt) REVERT: O 201 ASP cc_start: 0.7424 (t0) cc_final: 0.7224 (t0) REVERT: O 304 ILE cc_start: 0.8516 (mp) cc_final: 0.8211 (mt) REVERT: O 335 MET cc_start: 0.8654 (tmm) cc_final: 0.8394 (tmm) REVERT: P 164 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5888 (mp0) REVERT: P 167 LYS cc_start: 0.6148 (mptt) cc_final: 0.5783 (mttp) REVERT: P 242 LYS cc_start: 0.5522 (tptp) cc_final: 0.4470 (pttm) outliers start: 82 outliers final: 36 residues processed: 358 average time/residue: 0.1793 time to fit residues: 104.4533 Evaluate side-chains 294 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 335 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 303 ASN Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 324 SER Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 164 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 121 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 294 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN I 17 ASN I 223 ASN L 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.139055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098472 restraints weight = 61637.502| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.23 r_work: 0.3353 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.7835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28093 Z= 0.160 Angle : 0.652 14.447 38281 Z= 0.331 Chirality : 0.045 0.308 4389 Planarity : 0.005 0.065 4745 Dihedral : 12.197 178.794 4355 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.03 % Favored : 92.91 % Rotamer: Outliers : 2.95 % Allowed : 22.44 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.15), residues: 3341 helix: 0.18 (0.15), residues: 1194 sheet: -0.35 (0.22), residues: 593 loop : -1.73 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 35 TYR 0.014 0.001 TYR I 286 PHE 0.049 0.002 PHE P 89 TRP 0.015 0.001 TRP H 105 HIS 0.009 0.001 HIS O 14 Details of bonding type rmsd covalent geometry : bond 0.00373 (28088) covalent geometry : angle 0.65124 (38271) SS BOND : bond 0.00435 ( 5) SS BOND : angle 1.50228 ( 10) hydrogen bonds : bond 0.03111 ( 867) hydrogen bonds : angle 4.48869 ( 2478) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 255 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 63 SER cc_start: 0.5670 (m) cc_final: 0.5026 (p) REVERT: C 111 MET cc_start: -0.0102 (mmm) cc_final: -0.0858 (ptt) REVERT: C 262 PHE cc_start: 0.6556 (t80) cc_final: 0.5937 (t80) REVERT: D 37 GLN cc_start: 0.6190 (OUTLIER) cc_final: 0.5514 (tp40) REVERT: D 105 TRP cc_start: 0.6195 (m100) cc_final: 0.5457 (m100) REVERT: E 16 VAL cc_start: 0.8387 (t) cc_final: 0.8040 (m) REVERT: E 29 ASP cc_start: 0.8091 (m-30) cc_final: 0.7464 (p0) REVERT: E 88 LYS cc_start: 0.8699 (mmmt) cc_final: 0.8392 (mmtt) REVERT: I 28 GLU cc_start: 0.7551 (tt0) cc_final: 0.7181 (tm-30) REVERT: I 183 MET cc_start: 0.5019 (ptm) cc_final: 0.4393 (mpp) REVERT: I 213 VAL cc_start: 0.6372 (m) cc_final: 0.6032 (p) REVERT: I 253 ASN cc_start: 0.8598 (t0) cc_final: 0.8057 (t0) REVERT: I 257 SER cc_start: 0.8054 (m) cc_final: 0.6795 (m) REVERT: I 288 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7908 (mp0) REVERT: I 293 ILE cc_start: 0.4901 (tp) cc_final: 0.4537 (mt) REVERT: J 54 MET cc_start: 0.8628 (tpp) cc_final: 0.8193 (tpp) REVERT: J 92 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.5922 (pp20) REVERT: J 316 ASP cc_start: 0.8313 (m-30) cc_final: 0.7917 (p0) REVERT: K 77 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8570 (p) REVERT: K 104 GLN cc_start: 0.8370 (pm20) cc_final: 0.8082 (mm-40) REVERT: K 202 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8588 (pp) REVERT: L 1 MET cc_start: 0.7102 (ttm) cc_final: 0.6825 (ttt) REVERT: L 183 MET cc_start: 0.6963 (pmm) cc_final: 0.6262 (ptt) REVERT: L 217 GLU cc_start: 0.7981 (tp30) cc_final: 0.7661 (pt0) REVERT: N 119 ASP cc_start: 0.7356 (t0) cc_final: 0.7103 (t0) REVERT: N 183 MET cc_start: 0.7998 (ppp) cc_final: 0.6934 (ppp) REVERT: N 245 MET cc_start: 0.8096 (mmm) cc_final: 0.7384 (ttm) REVERT: O 1 MET cc_start: 0.7229 (tpp) cc_final: 0.6766 (tpt) REVERT: O 201 ASP cc_start: 0.7547 (t0) cc_final: 0.7329 (t0) REVERT: O 209 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: O 304 ILE cc_start: 0.8630 (mp) cc_final: 0.8345 (mt) REVERT: O 335 MET cc_start: 0.8587 (tmm) cc_final: 0.8305 (tmm) REVERT: P 164 GLU cc_start: 0.6118 (OUTLIER) cc_final: 0.5751 (mp0) REVERT: P 167 LYS cc_start: 0.6151 (mptt) cc_final: 0.5800 (mttp) outliers start: 83 outliers final: 54 residues processed: 322 average time/residue: 0.1806 time to fit residues: 95.0075 Evaluate side-chains 302 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 326 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 245 MET Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 209 GLN Chi-restraints excluded: chain O residue 303 ASN Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 324 SER Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 179 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 294 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN M 12 ASN N 162 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.137244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096212 restraints weight = 62538.246| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.39 r_work: 0.3313 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.8214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28093 Z= 0.181 Angle : 0.664 13.973 38281 Z= 0.337 Chirality : 0.046 0.364 4389 Planarity : 0.005 0.069 4745 Dihedral : 12.189 179.463 4355 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.97 % Favored : 92.97 % Rotamer: Outliers : 3.41 % Allowed : 22.65 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.15), residues: 3341 helix: 0.24 (0.15), residues: 1209 sheet: -0.37 (0.22), residues: 582 loop : -1.73 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 35 TYR 0.017 0.001 TYR H 14 PHE 0.023 0.002 PHE P 89 TRP 0.024 0.002 TRP J 42 HIS 0.007 0.001 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00425 (28088) covalent geometry : angle 0.66391 (38271) SS BOND : bond 0.00212 ( 5) SS BOND : angle 1.56288 ( 10) hydrogen bonds : bond 0.03134 ( 867) hydrogen bonds : angle 4.51605 ( 2478) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 255 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 PHE cc_start: 0.6454 (t80) cc_final: 0.5847 (t80) REVERT: D 37 GLN cc_start: 0.6508 (OUTLIER) cc_final: 0.5831 (tp40) REVERT: D 105 TRP cc_start: 0.6482 (m100) cc_final: 0.5638 (m100) REVERT: E 16 VAL cc_start: 0.8484 (t) cc_final: 0.8222 (m) REVERT: H 75 GLU cc_start: 0.6624 (tt0) cc_final: 0.6019 (mm-30) REVERT: H 88 LYS cc_start: 0.8515 (mmmt) cc_final: 0.7788 (tttm) REVERT: I 28 GLU cc_start: 0.7605 (tt0) cc_final: 0.7263 (tm-30) REVERT: I 149 LYS cc_start: 0.6286 (mmtt) cc_final: 0.6078 (mmpt) REVERT: I 183 MET cc_start: 0.5180 (ptm) cc_final: 0.4539 (mpp) REVERT: I 205 VAL cc_start: 0.6651 (t) cc_final: 0.6354 (t) REVERT: I 213 VAL cc_start: 0.6241 (m) cc_final: 0.5875 (p) REVERT: I 230 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6070 (pp20) REVERT: I 253 ASN cc_start: 0.8680 (t0) cc_final: 0.8209 (t0) REVERT: I 257 SER cc_start: 0.8104 (m) cc_final: 0.6872 (m) REVERT: I 288 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7995 (mp0) REVERT: I 293 ILE cc_start: 0.5129 (tp) cc_final: 0.4774 (mt) REVERT: J 54 MET cc_start: 0.8488 (tpp) cc_final: 0.8209 (tpt) REVERT: J 92 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6169 (pp20) REVERT: J 316 ASP cc_start: 0.8390 (m-30) cc_final: 0.7900 (p0) REVERT: K 77 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8512 (p) REVERT: K 104 GLN cc_start: 0.8489 (pm20) cc_final: 0.8179 (mm-40) REVERT: K 155 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7241 (tpt170) REVERT: K 202 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8651 (pp) REVERT: L 1 MET cc_start: 0.7162 (ttm) cc_final: 0.6883 (ttt) REVERT: L 183 MET cc_start: 0.7074 (pmm) cc_final: 0.6394 (ptt) REVERT: L 217 GLU cc_start: 0.7975 (tp30) cc_final: 0.7741 (pt0) REVERT: N 119 ASP cc_start: 0.7348 (t0) cc_final: 0.7040 (t0) REVERT: N 183 MET cc_start: 0.8082 (ppp) cc_final: 0.7004 (ppp) REVERT: O 1 MET cc_start: 0.7318 (tpp) cc_final: 0.6884 (tpt) REVERT: O 201 ASP cc_start: 0.7566 (t0) cc_final: 0.7321 (t0) REVERT: O 209 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: O 304 ILE cc_start: 0.8724 (mp) cc_final: 0.8463 (mt) REVERT: O 334 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8382 (ptpp) REVERT: O 335 MET cc_start: 0.8564 (tmm) cc_final: 0.8300 (tmm) REVERT: P 141 MET cc_start: 0.3554 (tmm) cc_final: 0.3260 (tmm) REVERT: P 164 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5615 (mp0) REVERT: P 167 LYS cc_start: 0.6066 (mptt) cc_final: 0.5697 (mttp) outliers start: 96 outliers final: 62 residues processed: 333 average time/residue: 0.1778 time to fit residues: 96.8463 Evaluate side-chains 309 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 239 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 293 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 209 GLN Chi-restraints excluded: chain O residue 303 ASN Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 324 SER Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 179 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 256 optimal weight: 5.9990 chunk 2 optimal weight: 30.0000 chunk 155 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 255 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN J 75 ASN J 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.133997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094791 restraints weight = 61883.273| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.17 r_work: 0.3238 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.8860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 28093 Z= 0.245 Angle : 0.735 15.885 38281 Z= 0.376 Chirality : 0.048 0.275 4389 Planarity : 0.006 0.175 4745 Dihedral : 12.268 179.774 4355 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.51 % Favored : 92.43 % Rotamer: Outliers : 3.37 % Allowed : 23.46 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.15), residues: 3341 helix: 0.19 (0.15), residues: 1180 sheet: -0.41 (0.22), residues: 555 loop : -1.86 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 37 TYR 0.025 0.002 TYR I 309 PHE 0.025 0.002 PHE M 88 TRP 0.046 0.003 TRP J 42 HIS 0.014 0.002 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00572 (28088) covalent geometry : angle 0.73466 (38271) SS BOND : bond 0.00174 ( 5) SS BOND : angle 1.47162 ( 10) hydrogen bonds : bond 0.03509 ( 867) hydrogen bonds : angle 4.66152 ( 2478) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 255 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LEU cc_start: 0.6486 (tp) cc_final: 0.6223 (tt) REVERT: C 111 MET cc_start: -0.1133 (mtt) cc_final: -0.1457 (ptt) REVERT: C 155 LEU cc_start: 0.0510 (OUTLIER) cc_final: 0.0246 (mt) REVERT: C 262 PHE cc_start: 0.6515 (t80) cc_final: 0.5844 (t80) REVERT: D 37 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6002 (tp-100) REVERT: D 105 TRP cc_start: 0.6635 (m100) cc_final: 0.5761 (m100) REVERT: E 88 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8551 (mmtt) REVERT: H 46 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8009 (mmtm) REVERT: H 75 GLU cc_start: 0.6645 (tt0) cc_final: 0.6119 (mm-30) REVERT: H 88 LYS cc_start: 0.8555 (mmmt) cc_final: 0.7940 (tttm) REVERT: I 17 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7727 (m110) REVERT: I 124 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7324 (pt) REVERT: I 183 MET cc_start: 0.5446 (ptm) cc_final: 0.4826 (mpp) REVERT: I 205 VAL cc_start: 0.6996 (t) cc_final: 0.6729 (t) REVERT: I 213 VAL cc_start: 0.6401 (m) cc_final: 0.5991 (p) REVERT: I 230 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6355 (pp20) REVERT: I 253 ASN cc_start: 0.8784 (t0) cc_final: 0.8323 (t0) REVERT: I 257 SER cc_start: 0.8338 (m) cc_final: 0.7198 (m) REVERT: I 293 ILE cc_start: 0.5530 (tp) cc_final: 0.5206 (mt) REVERT: I 316 ASP cc_start: 0.7637 (p0) cc_final: 0.7399 (p0) REVERT: J 92 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6265 (pp20) REVERT: J 223 ASN cc_start: 0.8187 (t0) cc_final: 0.7951 (t0) REVERT: K 77 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8609 (p) REVERT: K 104 GLN cc_start: 0.8479 (pm20) cc_final: 0.8185 (mm-40) REVERT: K 155 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.7307 (tpt170) REVERT: K 202 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8725 (pp) REVERT: L 1 MET cc_start: 0.7331 (ttm) cc_final: 0.6963 (ttt) REVERT: L 183 MET cc_start: 0.7282 (pmm) cc_final: 0.6576 (ptt) REVERT: N 119 ASP cc_start: 0.7403 (t0) cc_final: 0.7136 (t0) REVERT: N 183 MET cc_start: 0.8023 (ppp) cc_final: 0.6903 (ppp) REVERT: N 245 MET cc_start: 0.8303 (mmm) cc_final: 0.7596 (ttm) REVERT: O 1 MET cc_start: 0.7397 (tpp) cc_final: 0.6979 (tpt) REVERT: O 201 ASP cc_start: 0.7729 (t0) cc_final: 0.7457 (t0) REVERT: O 209 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: O 335 MET cc_start: 0.8721 (tmm) cc_final: 0.8408 (tmm) REVERT: P 141 MET cc_start: 0.3744 (tmm) cc_final: 0.3335 (tmm) REVERT: P 148 ASP cc_start: 0.7819 (p0) cc_final: 0.7574 (p0) REVERT: P 167 LYS cc_start: 0.6101 (mptt) cc_final: 0.5868 (mmtt) outliers start: 95 outliers final: 65 residues processed: 340 average time/residue: 0.1810 time to fit residues: 100.7731 Evaluate side-chains 309 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 235 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 293 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 209 GLN Chi-restraints excluded: chain O residue 303 ASN Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 324 SER Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 179 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 86 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 267 optimal weight: 0.2980 chunk 90 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 263 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.136011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096079 restraints weight = 61277.906| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.23 r_work: 0.3300 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.8953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28093 Z= 0.146 Angle : 0.668 14.529 38281 Z= 0.336 Chirality : 0.046 0.349 4389 Planarity : 0.004 0.056 4745 Dihedral : 12.221 179.939 4355 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.50 % Favored : 93.45 % Rotamer: Outliers : 2.77 % Allowed : 24.35 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.15), residues: 3341 helix: 0.40 (0.16), residues: 1181 sheet: -0.16 (0.23), residues: 540 loop : -1.82 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 35 TYR 0.020 0.001 TYR I 309 PHE 0.036 0.002 PHE C 288 TRP 0.040 0.002 TRP J 42 HIS 0.007 0.001 HIS O 14 Details of bonding type rmsd covalent geometry : bond 0.00337 (28088) covalent geometry : angle 0.66776 (38271) SS BOND : bond 0.00101 ( 5) SS BOND : angle 1.37782 ( 10) hydrogen bonds : bond 0.03036 ( 867) hydrogen bonds : angle 4.50267 ( 2478) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 247 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LEU cc_start: 0.6796 (tp) cc_final: 0.6566 (tt) REVERT: C 111 MET cc_start: -0.1239 (mtt) cc_final: -0.1603 (ptt) REVERT: C 155 LEU cc_start: 0.0420 (OUTLIER) cc_final: 0.0204 (mt) REVERT: C 262 PHE cc_start: 0.6665 (t80) cc_final: 0.6134 (t80) REVERT: D 37 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6000 (tp40) REVERT: D 105 TRP cc_start: 0.6504 (m100) cc_final: 0.5891 (m100) REVERT: E 88 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8426 (mmtt) REVERT: F 17 ASP cc_start: 0.7813 (p0) cc_final: 0.7565 (p0) REVERT: H 46 LYS cc_start: 0.8600 (ttmm) cc_final: 0.7878 (mmtm) REVERT: H 88 LYS cc_start: 0.8583 (mmmt) cc_final: 0.7971 (tttm) REVERT: I 106 ASN cc_start: 0.8918 (m110) cc_final: 0.8589 (p0) REVERT: I 183 MET cc_start: 0.5353 (ptm) cc_final: 0.4800 (mpp) REVERT: I 205 VAL cc_start: 0.6991 (t) cc_final: 0.6716 (t) REVERT: I 230 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6061 (pp20) REVERT: I 253 ASN cc_start: 0.8775 (t0) cc_final: 0.8358 (t0) REVERT: I 257 SER cc_start: 0.8280 (m) cc_final: 0.7118 (m) REVERT: I 288 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8110 (mp0) REVERT: I 293 ILE cc_start: 0.5593 (tp) cc_final: 0.5303 (mt) REVERT: I 316 ASP cc_start: 0.7695 (p0) cc_final: 0.7453 (p0) REVERT: J 92 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6188 (pp20) REVERT: J 223 ASN cc_start: 0.8095 (t0) cc_final: 0.7869 (t0) REVERT: J 245 MET cc_start: 0.7758 (tpp) cc_final: 0.7486 (mmm) REVERT: K 77 THR cc_start: 0.8759 (m) cc_final: 0.8475 (p) REVERT: K 104 GLN cc_start: 0.8470 (pm20) cc_final: 0.8116 (mm-40) REVERT: K 155 ARG cc_start: 0.7712 (mtt-85) cc_final: 0.7300 (tpt170) REVERT: K 202 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8657 (pp) REVERT: L 1 MET cc_start: 0.7164 (ttm) cc_final: 0.6871 (ttt) REVERT: L 183 MET cc_start: 0.7206 (pmm) cc_final: 0.6503 (ptt) REVERT: N 119 ASP cc_start: 0.7264 (t0) cc_final: 0.6993 (t0) REVERT: N 183 MET cc_start: 0.8020 (ppp) cc_final: 0.6913 (ppp) REVERT: N 245 MET cc_start: 0.8263 (mmm) cc_final: 0.7937 (ttm) REVERT: O 1 MET cc_start: 0.7254 (tpp) cc_final: 0.6808 (tpt) REVERT: O 201 ASP cc_start: 0.7737 (t0) cc_final: 0.7461 (t0) REVERT: O 209 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: O 335 MET cc_start: 0.8735 (tmm) cc_final: 0.8419 (tmm) REVERT: P 141 MET cc_start: 0.3801 (tmm) cc_final: 0.3456 (tmm) REVERT: P 143 ILE cc_start: 0.7351 (mm) cc_final: 0.6815 (tp) REVERT: P 148 ASP cc_start: 0.7663 (p0) cc_final: 0.7424 (p0) REVERT: P 164 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.5578 (mp0) REVERT: P 167 LYS cc_start: 0.6113 (mptt) cc_final: 0.5733 (ttmt) outliers start: 78 outliers final: 58 residues processed: 318 average time/residue: 0.1771 time to fit residues: 92.5432 Evaluate side-chains 301 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 293 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 209 GLN Chi-restraints excluded: chain O residue 303 ASN Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 324 SER Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 124 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 0.0020 chunk 256 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 305 optimal weight: 0.0670 chunk 328 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 overall best weight: 1.6132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.134248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093709 restraints weight = 62537.251| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.45 r_work: 0.3255 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.9079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28093 Z= 0.165 Angle : 0.670 14.786 38281 Z= 0.337 Chirality : 0.046 0.350 4389 Planarity : 0.004 0.058 4745 Dihedral : 12.192 179.510 4355 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.61 % Rotamer: Outliers : 2.77 % Allowed : 24.53 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.15), residues: 3341 helix: 0.43 (0.16), residues: 1181 sheet: -0.16 (0.23), residues: 544 loop : -1.80 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 35 TYR 0.020 0.001 TYR I 309 PHE 0.029 0.002 PHE C 288 TRP 0.071 0.002 TRP J 42 HIS 0.007 0.001 HIS O 14 Details of bonding type rmsd covalent geometry : bond 0.00388 (28088) covalent geometry : angle 0.66940 (38271) SS BOND : bond 0.00091 ( 5) SS BOND : angle 1.35315 ( 10) hydrogen bonds : bond 0.03094 ( 867) hydrogen bonds : angle 4.47788 ( 2478) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 253 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 MET cc_start: -0.1140 (mtt) cc_final: -0.1502 (ptt) REVERT: C 155 LEU cc_start: 0.0462 (OUTLIER) cc_final: 0.0222 (mt) REVERT: C 262 PHE cc_start: 0.6594 (t80) cc_final: 0.6007 (t80) REVERT: D 37 GLN cc_start: 0.6814 (OUTLIER) cc_final: 0.5940 (tp40) REVERT: D 105 TRP cc_start: 0.6736 (m100) cc_final: 0.6046 (m100) REVERT: E 88 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8476 (mmtt) REVERT: F 17 ASP cc_start: 0.7823 (p0) cc_final: 0.7563 (p0) REVERT: G 49 ARG cc_start: 0.8789 (ttt90) cc_final: 0.8426 (ttt180) REVERT: H 46 LYS cc_start: 0.8611 (ttmm) cc_final: 0.7936 (mmtm) REVERT: H 88 LYS cc_start: 0.8547 (mmmt) cc_final: 0.7951 (tttm) REVERT: I 28 GLU cc_start: 0.7867 (tt0) cc_final: 0.7124 (tm-30) REVERT: I 31 LYS cc_start: 0.8584 (mmtt) cc_final: 0.7998 (mmmt) REVERT: I 106 ASN cc_start: 0.8871 (m110) cc_final: 0.8545 (p0) REVERT: I 166 ASP cc_start: 0.3949 (t70) cc_final: 0.3684 (t70) REVERT: I 183 MET cc_start: 0.5568 (ptm) cc_final: 0.5090 (mpp) REVERT: I 213 VAL cc_start: 0.6453 (OUTLIER) cc_final: 0.6057 (p) REVERT: I 253 ASN cc_start: 0.8791 (t0) cc_final: 0.8435 (t0) REVERT: I 257 SER cc_start: 0.8306 (m) cc_final: 0.7179 (m) REVERT: I 288 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8127 (mp0) REVERT: I 293 ILE cc_start: 0.5767 (tp) cc_final: 0.5467 (mt) REVERT: I 316 ASP cc_start: 0.7543 (p0) cc_final: 0.7273 (p0) REVERT: J 90 GLN cc_start: 0.8180 (mt0) cc_final: 0.7807 (mt0) REVERT: J 92 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6282 (pp20) REVERT: J 223 ASN cc_start: 0.8238 (t0) cc_final: 0.8017 (t0) REVERT: K 77 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8510 (p) REVERT: K 104 GLN cc_start: 0.8532 (pm20) cc_final: 0.8194 (mm-40) REVERT: K 155 ARG cc_start: 0.7727 (mtt-85) cc_final: 0.7317 (tpt170) REVERT: K 202 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8677 (pp) REVERT: K 294 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8690 (mt) REVERT: L 1 MET cc_start: 0.7294 (ttm) cc_final: 0.6971 (ttt) REVERT: L 183 MET cc_start: 0.7178 (pmm) cc_final: 0.6428 (ptt) REVERT: N 119 ASP cc_start: 0.7356 (t0) cc_final: 0.7061 (t0) REVERT: N 183 MET cc_start: 0.8127 (ppp) cc_final: 0.6993 (ppp) REVERT: N 245 MET cc_start: 0.8356 (mmm) cc_final: 0.8035 (ttm) REVERT: O 1 MET cc_start: 0.7323 (tpp) cc_final: 0.6882 (tpt) REVERT: O 201 ASP cc_start: 0.7788 (t0) cc_final: 0.7510 (t0) REVERT: O 209 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: O 335 MET cc_start: 0.8741 (tmm) cc_final: 0.8442 (tmm) REVERT: P 141 MET cc_start: 0.3963 (tmm) cc_final: 0.3726 (tmm) REVERT: P 143 ILE cc_start: 0.7458 (mm) cc_final: 0.7137 (mm) REVERT: P 148 ASP cc_start: 0.7766 (p0) cc_final: 0.7073 (p0) REVERT: P 150 GLU cc_start: 0.6004 (mm-30) cc_final: 0.5677 (mp0) REVERT: P 164 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5599 (mp0) REVERT: P 167 LYS cc_start: 0.6101 (mptt) cc_final: 0.5729 (ttmt) outliers start: 78 outliers final: 60 residues processed: 328 average time/residue: 0.1827 time to fit residues: 97.2509 Evaluate side-chains 311 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 242 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 293 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 209 GLN Chi-restraints excluded: chain O residue 303 ASN Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 324 SER Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 162 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 325 optimal weight: 0.0970 chunk 104 optimal weight: 0.0670 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 315 optimal weight: 0.0030 chunk 257 optimal weight: 0.9980 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 ASN I 223 ASN K 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.138053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098347 restraints weight = 60875.762| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.24 r_work: 0.3348 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.9095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28093 Z= 0.115 Angle : 0.647 14.705 38281 Z= 0.322 Chirality : 0.044 0.350 4389 Planarity : 0.004 0.063 4745 Dihedral : 12.212 178.468 4355 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 1.77 % Allowed : 25.74 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.15), residues: 3341 helix: 0.50 (0.16), residues: 1187 sheet: -0.06 (0.23), residues: 546 loop : -1.76 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 35 TYR 0.023 0.001 TYR I 309 PHE 0.032 0.001 PHE C 288 TRP 0.055 0.002 TRP J 42 HIS 0.008 0.001 HIS O 14 Details of bonding type rmsd covalent geometry : bond 0.00254 (28088) covalent geometry : angle 0.64649 (38271) SS BOND : bond 0.00142 ( 5) SS BOND : angle 1.19119 ( 10) hydrogen bonds : bond 0.02824 ( 867) hydrogen bonds : angle 4.35101 ( 2478) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7678.90 seconds wall clock time: 132 minutes 25.81 seconds (7945.81 seconds total)