Starting phenix.real_space_refine on Mon Jun 23 19:56:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tr6_26081/06_2025/7tr6_26081_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tr6_26081/06_2025/7tr6_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_26081/06_2025/7tr6_26081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tr6_26081/06_2025/7tr6_26081.map" model { file = "/net/cci-nas-00/data/ceres_data/7tr6_26081/06_2025/7tr6_26081_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tr6_26081/06_2025/7tr6_26081_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: 16.39, per 1000 atoms: 0.60 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: 7.39 Conformation dependent library (CDL) restraints added in 4.0 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: 9.04 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: 8.67 Time building geometry restraints manager: 8.37 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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 66.170 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.120 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP H 105 HIS 0.006 0.001 HIS L 162 PHE 0.013 0.001 PHE C 54 TYR 0.018 0.001 TYR C 157 ARG 0.007 0.000 ARG J 131 Details of bonding type rmsd hydrogen bonds : bond 0.15472 ( 867) hydrogen bonds : angle 5.95984 ( 2478) SS BOND : bond 0.00032 ( 5) SS BOND : angle 0.64967 ( 10) covalent geometry : bond 0.00275 (28088) covalent geometry : angle 0.57425 (38271) *********************** 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 : 2.870 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: -0.0553 (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: 0.2257 (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: 0.2318 (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: 0.6444 (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: 0.7248 (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: 0.4096 (mt) REVERT: J 202 LEU cc_start: 0.4804 (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: 0.3441 (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: 0.4368 time to fit residues: 495.0027 Evaluate side-chains 363 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 304 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN K 17 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 HIS L 229 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.156720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.121763 restraints weight = 63902.307| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.44 r_work: 0.3689 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3238 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= 0.169 Angle : 0.705 16.990 38281 Z= 0.356 Chirality : 0.048 0.267 4389 Planarity : 0.006 0.120 4745 Dihedral : 12.214 177.034 4355 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 2.52 % Allowed : 12.21 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3341 helix: 0.23 (0.16), residues: 1156 sheet: 0.01 (0.23), residues: 521 loop : -1.56 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 58 HIS 0.010 0.002 HIS C 56 PHE 0.029 0.002 PHE K 185 TYR 0.026 0.002 TYR D 14 ARG 0.009 0.001 ARG N 291 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 867) hydrogen bonds : angle 4.75701 ( 2478) SS BOND : bond 0.00080 ( 5) SS BOND : angle 0.54342 ( 10) covalent geometry : bond 0.00381 (28088) covalent geometry : angle 0.70479 (38271) *********************** 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 486 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 415 time to evaluate : 2.995 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: C 63 SER cc_start: 0.5723 (m) cc_final: 0.5091 (p) REVERT: C 111 MET cc_start: 0.0076 (mmm) cc_final: -0.0596 (ptt) REVERT: C 191 GLU cc_start: 0.6400 (mm-30) cc_final: 0.6009 (mt-10) REVERT: C 262 PHE cc_start: 0.6120 (t80) cc_final: 0.5607 (t80) REVERT: C 264 GLU cc_start: 0.4206 (tp30) cc_final: 0.4004 (mm-30) REVERT: C 271 MET cc_start: -0.0006 (ttt) cc_final: -0.0242 (tmm) REVERT: C 283 TYR cc_start: 0.5637 (t80) cc_final: 0.5050 (p90) REVERT: D 5 ILE cc_start: 0.3048 (OUTLIER) cc_final: 0.2821 (tp) REVERT: D 46 LYS cc_start: 0.8289 (mmmm) cc_final: 0.7990 (mttp) REVERT: E 78 GLU cc_start: 0.6638 (tp30) cc_final: 0.5694 (tt0) REVERT: H 72 GLU cc_start: 0.8564 (tp30) cc_final: 0.7911 (mp0) REVERT: H 75 GLU cc_start: 0.6464 (tt0) cc_final: 0.6152 (mm-30) REVERT: I 108 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7588 (tt0) REVERT: I 183 MET cc_start: 0.4248 (ptm) cc_final: 0.3848 (ptp) REVERT: I 288 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7708 (mp0) REVERT: I 293 ILE cc_start: 0.3656 (tp) cc_final: 0.3357 (mt) REVERT: J 1 MET cc_start: 0.7625 (mmm) cc_final: 0.7263 (tpp) REVERT: J 316 ASP cc_start: 0.8458 (m-30) cc_final: 0.7870 (p0) REVERT: N 226 ILE cc_start: 0.7458 (pt) cc_final: 0.7228 (pt) REVERT: O 10 ARG cc_start: 0.6870 (ttm170) cc_final: 0.5145 (tmm160) REVERT: O 67 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6517 (t80) REVERT: O 82 ARG cc_start: 0.6928 (ptp90) cc_final: 0.5285 (mmt180) REVERT: O 211 LEU cc_start: 0.6780 (tp) cc_final: 0.6393 (mp) REVERT: P 98 GLU cc_start: 0.1968 (pm20) cc_final: -0.0421 (tm-30) REVERT: P 141 MET cc_start: 0.3019 (ttp) cc_final: 0.2584 (tmm) REVERT: P 216 ILE cc_start: 0.6311 (mp) cc_final: 0.6091 (tt) REVERT: P 242 LYS cc_start: 0.5440 (tptp) cc_final: 0.4461 (pttp) outliers start: 71 outliers final: 43 residues processed: 470 average time/residue: 0.4046 time to fit residues: 301.3702 Evaluate side-chains 354 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 309 time to evaluate : 3.057 ------------------------------------------------------------------------------- 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 5 ILE 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 H residue 28 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 76 LEU 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 308 THR 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 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 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 67 PHE Chi-restraints excluded: chain O residue 76 LEU 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 12 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 244 optimal weight: 0.1980 chunk 93 optimal weight: 20.0000 chunk 196 optimal weight: 0.2980 chunk 324 optimal weight: 0.0370 chunk 165 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- 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** I 17 ASN K 17 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 HIS L 12 ASN L 53 ASN ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 310 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.147941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.110657 restraints weight = 62659.792| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.51 r_work: 0.3509 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 28093 Z= 0.201 Angle : 0.700 10.588 38281 Z= 0.358 Chirality : 0.047 0.257 4389 Planarity : 0.006 0.145 4745 Dihedral : 12.267 175.588 4355 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 3.37 % Allowed : 16.93 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3341 helix: -0.01 (0.15), residues: 1187 sheet: -0.24 (0.23), residues: 533 loop : -1.56 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP F 105 HIS 0.009 0.002 HIS I 162 PHE 0.027 0.002 PHE J 261 TYR 0.027 0.002 TYR P 20 ARG 0.025 0.001 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 867) hydrogen bonds : angle 4.73279 ( 2478) SS BOND : bond 0.00140 ( 5) SS BOND : angle 1.08020 ( 10) covalent geometry : bond 0.00464 (28088) covalent geometry : angle 0.69970 (38271) *********************** 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 436 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 341 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 SER cc_start: 0.5823 (m) cc_final: 0.5546 (p) REVERT: C 259 ILE cc_start: 0.3574 (mt) cc_final: 0.3305 (tt) REVERT: C 262 PHE cc_start: 0.6129 (t80) cc_final: 0.5743 (t80) REVERT: C 283 TYR cc_start: 0.5728 (t80) cc_final: 0.5079 (p90) REVERT: D 105 TRP cc_start: 0.6077 (m100) cc_final: 0.5427 (m100) REVERT: E 29 ASP cc_start: 0.8090 (m-30) cc_final: 0.7634 (p0) REVERT: H 75 GLU cc_start: 0.6298 (tt0) cc_final: 0.5823 (mm-30) REVERT: H 79 GLU cc_start: 0.8227 (pm20) cc_final: 0.7886 (mm-30) REVERT: I 111 ILE cc_start: 0.8168 (mm) cc_final: 0.7963 (mm) REVERT: I 183 MET cc_start: 0.4696 (ptm) cc_final: 0.4334 (ptp) REVERT: I 257 SER cc_start: 0.7147 (m) cc_final: 0.6726 (m) REVERT: I 276 PRO cc_start: 0.4254 (Cg_endo) cc_final: 0.3804 (Cg_exo) REVERT: I 288 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7794 (mp0) REVERT: I 293 ILE cc_start: 0.3941 (tp) cc_final: 0.3570 (mt) REVERT: I 305 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5832 (tp30) REVERT: J 26 TYR cc_start: 0.6178 (t80) cc_final: 0.5638 (t80) REVERT: J 316 ASP cc_start: 0.8390 (m-30) cc_final: 0.8023 (p0) REVERT: L 310 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8121 (p0) REVERT: N 130 ARG cc_start: 0.7251 (mmp80) cc_final: 0.6851 (mmp80) REVERT: N 227 ASP cc_start: 0.7683 (t0) cc_final: 0.7310 (t0) REVERT: O 10 ARG cc_start: 0.7577 (ttm170) cc_final: 0.5843 (ptt180) REVERT: O 30 THR cc_start: 0.6762 (p) cc_final: 0.6537 (t) REVERT: O 67 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.6677 (t80) REVERT: O 82 ARG cc_start: 0.7154 (ptp90) cc_final: 0.5826 (mmt180) REVERT: O 201 ASP cc_start: 0.6821 (t0) cc_final: 0.6546 (t0) REVERT: O 245 MET cc_start: 0.6908 (mtp) cc_final: 0.6375 (ttm) REVERT: P 98 GLU cc_start: 0.1001 (pm20) cc_final: -0.0746 (tm-30) REVERT: P 216 ILE cc_start: 0.6543 (mp) cc_final: 0.6317 (tt) REVERT: P 242 LYS cc_start: 0.5544 (tptp) cc_final: 0.4555 (pttp) outliers start: 95 outliers final: 48 residues processed: 414 average time/residue: 0.3696 time to fit residues: 244.7556 Evaluate side-chains 324 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 2.736 ------------------------------------------------------------------------------- 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 90 LEU Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 305 GLU 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 142 LEU Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 335 MET 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 293 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 L residue 310 ASN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 186 SER Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 198 ILE Chi-restraints excluded: chain N residue 239 LEU Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 74 VAL 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 266 LEU Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain O residue 325 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 90 optimal weight: 7.9990 chunk 169 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 303 optimal weight: 0.3980 chunk 55 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 262 optimal weight: 0.6980 chunk 289 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** I 17 ASN ** I 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN N 253 ASN O 14 HIS ** O 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.148294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.108286 restraints weight = 62938.619| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.27 r_work: 0.3529 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28093 Z= 0.126 Angle : 0.616 13.641 38281 Z= 0.311 Chirality : 0.044 0.264 4389 Planarity : 0.005 0.059 4745 Dihedral : 12.189 176.483 4355 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.06 % Favored : 92.88 % Rotamer: Outliers : 2.66 % Allowed : 19.70 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3341 helix: 0.17 (0.15), residues: 1193 sheet: -0.10 (0.22), residues: 539 loop : -1.58 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 105 HIS 0.006 0.001 HIS L 57 PHE 0.023 0.001 PHE J 261 TYR 0.016 0.001 TYR D 14 ARG 0.008 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.03077 ( 867) hydrogen bonds : angle 4.44703 ( 2478) SS BOND : bond 0.00596 ( 5) SS BOND : angle 1.64646 ( 10) covalent geometry : bond 0.00287 (28088) covalent geometry : angle 0.61595 (38271) *********************** 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 359 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 284 time to evaluate : 3.048 Fit side-chains revert: symmetry clash REVERT: C 63 SER cc_start: 0.5792 (m) cc_final: 0.5201 (p) REVERT: C 111 MET cc_start: 0.0142 (mmm) cc_final: -0.0573 (ptt) REVERT: C 262 PHE cc_start: 0.6395 (t80) cc_final: 0.5951 (t80) REVERT: D 105 TRP cc_start: 0.6181 (m100) cc_final: 0.5915 (m100) REVERT: E 29 ASP cc_start: 0.8092 (m-30) cc_final: 0.7615 (p0) REVERT: E 79 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7172 (mm-30) REVERT: I 111 ILE cc_start: 0.8173 (mm) cc_final: 0.7937 (mm) REVERT: I 149 LYS cc_start: 0.5136 (mttm) cc_final: 0.4874 (pptt) REVERT: I 183 MET cc_start: 0.4651 (ptm) cc_final: 0.4323 (ptp) REVERT: I 245 MET cc_start: 0.5756 (mmt) cc_final: 0.5371 (mmm) REVERT: I 253 ASN cc_start: 0.7821 (t0) cc_final: 0.7546 (t0) REVERT: I 265 GLU cc_start: 0.4874 (tt0) cc_final: 0.4459 (tt0) REVERT: I 276 PRO cc_start: 0.4343 (Cg_endo) cc_final: 0.4112 (Cg_exo) REVERT: I 288 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7785 (mp0) REVERT: I 293 ILE cc_start: 0.3970 (tp) cc_final: 0.3555 (mt) REVERT: J 26 TYR cc_start: 0.6048 (t80) cc_final: 0.5847 (t80) REVERT: J 316 ASP cc_start: 0.8291 (m-30) cc_final: 0.7942 (p0) REVERT: N 227 ASP cc_start: 0.7793 (t0) cc_final: 0.7477 (t0) REVERT: O 10 ARG cc_start: 0.7474 (ttm170) cc_final: 0.5702 (ptt90) REVERT: O 67 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6886 (t80) REVERT: O 82 ARG cc_start: 0.7169 (ptp90) cc_final: 0.5907 (mmt180) REVERT: O 201 ASP cc_start: 0.6704 (t0) cc_final: 0.6438 (t0) REVERT: O 245 MET cc_start: 0.6711 (mtp) cc_final: 0.6276 (ttm) REVERT: P 98 GLU cc_start: 0.1185 (pm20) cc_final: -0.0571 (tm-30) REVERT: P 109 MET cc_start: -0.0136 (tpt) cc_final: -0.0445 (tpt) REVERT: P 216 ILE cc_start: 0.6552 (mp) cc_final: 0.6337 (tt) REVERT: P 242 LYS cc_start: 0.5558 (tptp) cc_final: 0.4619 (pttm) outliers start: 75 outliers final: 45 residues processed: 347 average time/residue: 0.3672 time to fit residues: 207.9591 Evaluate side-chains 300 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 97 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 328 LEU 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 142 LEU 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 77 THR Chi-restraints excluded: chain K residue 110 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 96 THR Chi-restraints excluded: chain L residue 286 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 253 ASN 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 86 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 226 ILE Chi-restraints excluded: chain O residue 286 TYR 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 P residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 216 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 101 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 HIS I 17 ASN ** I 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN K 17 ASN K 53 ASN ** K 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN N 53 ASN O 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.138606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097319 restraints weight = 62098.581| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.31 r_work: 0.3339 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 28093 Z= 0.250 Angle : 0.753 13.284 38281 Z= 0.390 Chirality : 0.049 0.304 4389 Planarity : 0.006 0.106 4745 Dihedral : 12.318 177.622 4355 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.87 % Favored : 92.07 % Rotamer: Outliers : 4.15 % Allowed : 19.35 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3341 helix: -0.10 (0.15), residues: 1200 sheet: -0.24 (0.22), residues: 546 loop : -1.76 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 100 HIS 0.011 0.002 HIS L 162 PHE 0.028 0.002 PHE J 60 TYR 0.024 0.002 TYR G 11 ARG 0.013 0.001 ARG M 187 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 867) hydrogen bonds : angle 4.68441 ( 2478) SS BOND : bond 0.01521 ( 5) SS BOND : angle 1.74485 ( 10) covalent geometry : bond 0.00589 (28088) covalent geometry : angle 0.75294 (38271) *********************** 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 415 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 298 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 PHE cc_start: 0.6466 (t80) cc_final: 0.5894 (t80) REVERT: D 105 TRP cc_start: 0.6326 (m100) cc_final: 0.5964 (m100) REVERT: E 18 ASP cc_start: 0.7665 (m-30) cc_final: 0.7380 (m-30) REVERT: E 88 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8430 (mmtt) REVERT: I 183 MET cc_start: 0.5107 (ptm) cc_final: 0.4466 (mpp) REVERT: I 230 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5971 (pp20) REVERT: I 253 ASN cc_start: 0.8148 (t0) cc_final: 0.7860 (t0) REVERT: I 276 PRO cc_start: 0.4377 (Cg_endo) cc_final: 0.4144 (Cg_exo) REVERT: I 288 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7842 (mp0) REVERT: I 293 ILE cc_start: 0.4263 (tp) cc_final: 0.3831 (mt) REVERT: I 305 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5727 (tp30) REVERT: J 1 MET cc_start: 0.8096 (tpp) cc_final: 0.7631 (tpp) REVERT: J 124 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8297 (tp) REVERT: J 316 ASP cc_start: 0.8392 (m-30) cc_final: 0.7891 (p0) REVERT: K 202 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8461 (pp) REVERT: K 293 ILE cc_start: 0.9443 (tt) cc_final: 0.9206 (tp) REVERT: L 1 MET cc_start: 0.7076 (ttm) cc_final: 0.6705 (ttt) REVERT: L 81 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8800 (mt) REVERT: M 326 GLU cc_start: 0.8220 (pp20) cc_final: 0.7843 (pp20) REVERT: N 183 MET cc_start: 0.7988 (ppp) cc_final: 0.6809 (ppp) REVERT: O 30 THR cc_start: 0.7357 (p) cc_final: 0.6878 (t) REVERT: O 245 MET cc_start: 0.7064 (mtp) cc_final: 0.6769 (ttm) REVERT: O 304 ILE cc_start: 0.8538 (mp) cc_final: 0.8241 (mt) REVERT: O 335 MET cc_start: 0.8654 (tmm) cc_final: 0.8442 (tmm) REVERT: P 98 GLU cc_start: 0.1248 (pm20) cc_final: 0.1037 (pm20) REVERT: P 109 MET cc_start: 0.0202 (tpt) cc_final: -0.0145 (tpt) REVERT: P 112 GLU cc_start: 0.0915 (OUTLIER) cc_final: 0.0461 (pt0) REVERT: P 167 LYS cc_start: 0.6119 (mptt) cc_final: 0.5785 (mttp) REVERT: P 200 MET cc_start: 0.4265 (OUTLIER) cc_final: 0.4023 (tmm) REVERT: P 216 ILE cc_start: 0.6691 (mp) cc_final: 0.6455 (tt) REVERT: P 242 LYS cc_start: 0.5406 (tptp) cc_final: 0.4339 (pttm) outliers start: 117 outliers final: 57 residues processed: 395 average time/residue: 0.4269 time to fit residues: 275.3134 Evaluate side-chains 312 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 248 time to evaluate : 4.629 ------------------------------------------------------------------------------- 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 223 LEU Chi-restraints excluded: chain C residue 226 LEU 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 28 VAL Chi-restraints excluded: chain D residue 90 LEU 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 12 LEU Chi-restraints excluded: chain H residue 28 VAL 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 117 ASP Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 305 GLU Chi-restraints excluded: chain J residue 61 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 137 LYS 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 335 MET Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 215 PHE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 316 ASP 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 M residue 5 ILE 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 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 86 THR Chi-restraints excluded: chain O residue 226 ILE 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 P residue 112 GLU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 200 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 306 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 chunk 181 optimal weight: 0.4980 chunk 253 optimal weight: 0.5980 chunk 289 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 ASN ** I 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN L 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.141611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.103115 restraints weight = 62000.550| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.38 r_work: 0.3378 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.7320 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= 0.125 Angle : 0.627 14.050 38281 Z= 0.319 Chirality : 0.045 0.273 4389 Planarity : 0.005 0.064 4745 Dihedral : 12.215 178.574 4355 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.73 % Favored : 93.21 % Rotamer: Outliers : 2.59 % Allowed : 21.41 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3341 helix: 0.08 (0.15), residues: 1202 sheet: -0.13 (0.22), residues: 547 loop : -1.74 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 105 HIS 0.005 0.001 HIS L 57 PHE 0.023 0.001 PHE I 88 TYR 0.017 0.001 TYR D 14 ARG 0.011 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 867) hydrogen bonds : angle 4.38714 ( 2478) SS BOND : bond 0.00166 ( 5) SS BOND : angle 1.25301 ( 10) covalent geometry : bond 0.00281 (28088) covalent geometry : angle 0.62658 (38271) *********************** 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 350 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 277 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 PHE cc_start: 0.6637 (t80) cc_final: 0.5937 (t80) REVERT: D 105 TRP cc_start: 0.6254 (m100) cc_final: 0.5506 (m100) REVERT: E 16 VAL cc_start: 0.8360 (t) cc_final: 0.7960 (m) REVERT: E 18 ASP cc_start: 0.7630 (m-30) cc_final: 0.7313 (m-30) REVERT: E 29 ASP cc_start: 0.8043 (m-30) cc_final: 0.7354 (p0) REVERT: I 16 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6392 (mt) REVERT: I 28 GLU cc_start: 0.7531 (tt0) cc_final: 0.7065 (tm-30) REVERT: I 183 MET cc_start: 0.4978 (ptm) cc_final: 0.4329 (mpp) REVERT: I 230 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6043 (pp20) REVERT: I 288 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7822 (mp0) REVERT: I 293 ILE cc_start: 0.4421 (tp) cc_final: 0.4062 (mt) REVERT: I 328 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7389 (tp) REVERT: J 1 MET cc_start: 0.8092 (tpp) cc_final: 0.7728 (tpp) REVERT: K 77 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8557 (p) REVERT: K 104 GLN cc_start: 0.8419 (pm20) cc_final: 0.8004 (mm-40) REVERT: K 293 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9022 (tt) REVERT: L 1 MET cc_start: 0.6984 (ttm) cc_final: 0.6653 (ttm) REVERT: L 81 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8566 (mt) REVERT: L 183 MET cc_start: 0.6833 (pmm) cc_final: 0.6069 (ptt) REVERT: L 217 GLU cc_start: 0.8084 (tp30) cc_final: 0.7550 (pt0) REVERT: N 183 MET cc_start: 0.7885 (ppp) cc_final: 0.6848 (ppp) REVERT: O 1 MET cc_start: 0.6720 (tpp) cc_final: 0.6362 (tpt) REVERT: O 201 ASP cc_start: 0.7377 (t0) cc_final: 0.7168 (t0) REVERT: P 141 MET cc_start: 0.3403 (tmm) cc_final: 0.3133 (tmm) REVERT: P 167 LYS cc_start: 0.6139 (mptt) cc_final: 0.5805 (mttp) REVERT: P 242 LYS cc_start: 0.5471 (tptp) cc_final: 0.4363 (pttp) outliers start: 73 outliers final: 34 residues processed: 330 average time/residue: 0.3760 time to fit residues: 200.6922 Evaluate side-chains 280 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 3.368 ------------------------------------------------------------------------------- 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 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 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 117 ASP Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 279 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 306 VAL 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 215 PHE Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 237 SER 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 N residue 311 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 286 TYR Chi-restraints excluded: chain O residue 303 ASN Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain P residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 69 optimal weight: 0.0770 chunk 334 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 223 ASN I 253 ASN J 162 HIS L 17 ASN N 253 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.140428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099991 restraints weight = 61723.696| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.29 r_work: 0.3369 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.7606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28093 Z= 0.141 Angle : 0.630 15.804 38281 Z= 0.320 Chirality : 0.045 0.317 4389 Planarity : 0.005 0.061 4745 Dihedral : 12.184 178.474 4355 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.70 % Favored : 93.24 % Rotamer: Outliers : 2.56 % Allowed : 22.40 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3341 helix: 0.24 (0.16), residues: 1208 sheet: -0.29 (0.22), residues: 571 loop : -1.76 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 58 HIS 0.005 0.001 HIS L 162 PHE 0.028 0.001 PHE C 288 TYR 0.015 0.001 TYR I 286 ARG 0.012 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 867) hydrogen bonds : angle 4.35202 ( 2478) SS BOND : bond 0.00128 ( 5) SS BOND : angle 1.56948 ( 10) covalent geometry : bond 0.00326 (28088) covalent geometry : angle 0.62911 (38271) *********************** 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 336 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 264 time to evaluate : 8.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LEU cc_start: 0.6699 (tp) cc_final: 0.6410 (tt) REVERT: C 262 PHE cc_start: 0.6659 (t80) cc_final: 0.6023 (t80) REVERT: D 105 TRP cc_start: 0.6048 (m100) cc_final: 0.5285 (m100) REVERT: E 16 VAL cc_start: 0.8339 (t) cc_final: 0.7956 (m) REVERT: E 18 ASP cc_start: 0.7736 (m-30) cc_final: 0.7437 (m-30) REVERT: E 29 ASP cc_start: 0.8055 (m-30) cc_final: 0.7394 (p0) REVERT: E 88 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8346 (mmtt) REVERT: H 29 ASP cc_start: 0.8673 (t0) cc_final: 0.8010 (m-30) REVERT: I 28 GLU cc_start: 0.7705 (tt0) cc_final: 0.7211 (tm-30) REVERT: I 183 MET cc_start: 0.5184 (ptm) cc_final: 0.4517 (mpp) REVERT: I 230 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6058 (pp20) REVERT: I 288 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7823 (mp0) REVERT: I 293 ILE cc_start: 0.4772 (tp) cc_final: 0.4404 (mt) REVERT: I 328 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7411 (tp) REVERT: J 1 MET cc_start: 0.8125 (tpp) cc_final: 0.7832 (tpp) REVERT: J 124 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8215 (tp) REVERT: J 316 ASP cc_start: 0.8319 (m-30) cc_final: 0.7868 (p0) REVERT: K 77 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8599 (p) REVERT: K 104 GLN cc_start: 0.8459 (pm20) cc_final: 0.8152 (mm110) REVERT: L 1 MET cc_start: 0.6990 (ttm) cc_final: 0.6586 (ttt) REVERT: L 27 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8819 (mt) REVERT: L 81 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8593 (mt) REVERT: L 183 MET cc_start: 0.6927 (pmm) cc_final: 0.6156 (ptt) REVERT: L 217 GLU cc_start: 0.7948 (tp30) cc_final: 0.7443 (pt0) REVERT: N 183 MET cc_start: 0.7892 (ppp) cc_final: 0.6901 (ppp) REVERT: N 245 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8069 (tpp) REVERT: O 1 MET cc_start: 0.6661 (tpp) cc_final: 0.6311 (tpt) REVERT: O 201 ASP cc_start: 0.7404 (t0) cc_final: 0.7168 (t0) REVERT: O 304 ILE cc_start: 0.8529 (mp) cc_final: 0.8238 (mt) REVERT: P 167 LYS cc_start: 0.6098 (mptt) cc_final: 0.5776 (mttp) outliers start: 72 outliers final: 51 residues processed: 318 average time/residue: 0.6079 time to fit residues: 320.1898 Evaluate side-chains 301 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 6.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 191 GLU 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 90 LEU 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 14 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 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 328 LEU Chi-restraints excluded: chain J residue 70 THR 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 278 LEU 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 77 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 215 PHE 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 316 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 237 SER 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 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 76 LEU Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 286 TYR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 151 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 chunk 246 optimal weight: 0.0670 chunk 229 optimal weight: 0.5980 chunk 328 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 75 ASN J 253 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 = 0.4174 r_free = 0.4174 target = 0.140318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.102161 restraints weight = 61458.078| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.38 r_work: 0.3354 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28093 Z= 0.137 Angle : 0.626 14.337 38281 Z= 0.318 Chirality : 0.045 0.376 4389 Planarity : 0.004 0.079 4745 Dihedral : 12.155 178.119 4355 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.76 % Favored : 93.18 % Rotamer: Outliers : 2.34 % Allowed : 23.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3341 helix: 0.31 (0.16), residues: 1209 sheet: -0.12 (0.22), residues: 566 loop : -1.73 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 42 HIS 0.005 0.001 HIS L 162 PHE 0.036 0.001 PHE C 288 TYR 0.014 0.001 TYR C 157 ARG 0.015 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.02859 ( 867) hydrogen bonds : angle 4.34298 ( 2478) SS BOND : bond 0.00216 ( 5) SS BOND : angle 1.27246 ( 10) covalent geometry : bond 0.00318 (28088) covalent geometry : angle 0.62586 (38271) *********************** 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 328 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 262 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LEU cc_start: 0.6387 (tp) cc_final: 0.6114 (tt) REVERT: C 111 MET cc_start: -0.0847 (mmm) cc_final: -0.1243 (ptt) REVERT: C 155 LEU cc_start: 0.0745 (OUTLIER) cc_final: 0.0431 (mt) REVERT: C 262 PHE cc_start: 0.6559 (t80) cc_final: 0.5906 (t80) REVERT: D 105 TRP cc_start: 0.6403 (m100) cc_final: 0.5612 (m100) REVERT: E 16 VAL cc_start: 0.8485 (t) cc_final: 0.8111 (m) REVERT: E 18 ASP cc_start: 0.7560 (m-30) cc_final: 0.7289 (m-30) REVERT: E 39 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: E 88 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8389 (mmtt) REVERT: G 49 ARG cc_start: 0.8635 (ttt180) cc_final: 0.8422 (ttt180) REVERT: H 29 ASP cc_start: 0.8299 (t0) cc_final: 0.7872 (m-30) REVERT: H 57 LYS cc_start: 0.7592 (tptp) cc_final: 0.6901 (tmtt) REVERT: I 28 GLU cc_start: 0.7660 (tt0) cc_final: 0.7242 (tm-30) REVERT: I 183 MET cc_start: 0.5262 (ptm) cc_final: 0.4573 (mpp) REVERT: I 230 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5996 (pp20) REVERT: I 288 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7979 (mp0) REVERT: I 293 ILE cc_start: 0.5105 (tp) cc_final: 0.4768 (mt) REVERT: I 328 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7542 (tp) REVERT: J 92 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5945 (pp20) REVERT: J 124 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8093 (tp) REVERT: J 316 ASP cc_start: 0.8315 (m-30) cc_final: 0.7861 (p0) REVERT: K 77 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8572 (p) REVERT: K 104 GLN cc_start: 0.8443 (pm20) cc_final: 0.8195 (mm110) REVERT: K 155 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.7140 (tpt170) REVERT: K 293 ILE cc_start: 0.9378 (tt) cc_final: 0.9149 (tt) REVERT: L 1 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6572 (ttm) REVERT: L 27 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8789 (mt) REVERT: L 81 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8557 (mt) REVERT: L 183 MET cc_start: 0.6885 (pmm) cc_final: 0.6151 (ptt) REVERT: L 217 GLU cc_start: 0.7953 (tp30) cc_final: 0.7615 (pt0) REVERT: N 183 MET cc_start: 0.7962 (ppp) cc_final: 0.7004 (ppp) REVERT: O 1 MET cc_start: 0.6694 (tpp) cc_final: 0.6411 (tpt) REVERT: O 201 ASP cc_start: 0.7538 (t0) cc_final: 0.7259 (t0) REVERT: O 304 ILE cc_start: 0.8599 (mp) cc_final: 0.8320 (mt) REVERT: O 335 MET cc_start: 0.8306 (tmm) cc_final: 0.7788 (ttm) REVERT: P 141 MET cc_start: 0.3449 (tmm) cc_final: 0.3176 (tmm) REVERT: P 167 LYS cc_start: 0.6094 (mptt) cc_final: 0.5759 (mttp) outliers start: 66 outliers final: 47 residues processed: 313 average time/residue: 0.3765 time to fit residues: 189.2377 Evaluate side-chains 298 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 155 LEU 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 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 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 230 GLU Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 328 LEU 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 278 LEU 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 77 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 215 PHE 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 L residue 1 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 17 ASN 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 N residue 245 MET Chi-restraints excluded: chain N residue 293 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 286 TYR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 7 optimal weight: 40.0000 chunk 97 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 170 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.139646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101523 restraints weight = 61627.010| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.55 r_work: 0.3344 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.8109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28093 Z= 0.138 Angle : 0.635 14.194 38281 Z= 0.320 Chirality : 0.044 0.341 4389 Planarity : 0.005 0.079 4745 Dihedral : 12.165 178.506 4355 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.03 % Favored : 92.91 % Rotamer: Outliers : 2.38 % Allowed : 23.46 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3341 helix: 0.43 (0.16), residues: 1179 sheet: -0.08 (0.22), residues: 564 loop : -1.75 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP J 42 HIS 0.005 0.001 HIS L 162 PHE 0.018 0.001 PHE C 273 TYR 0.017 0.001 TYR D 14 ARG 0.012 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.02851 ( 867) hydrogen bonds : angle 4.32317 ( 2478) SS BOND : bond 0.00145 ( 5) SS BOND : angle 1.19792 ( 10) covalent geometry : bond 0.00322 (28088) covalent geometry : angle 0.63439 (38271) *********************** 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 326 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 259 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LEU cc_start: 0.6465 (tp) cc_final: 0.6212 (tt) REVERT: C 111 MET cc_start: -0.0780 (mmm) cc_final: -0.1198 (ptt) REVERT: C 155 LEU cc_start: 0.0559 (OUTLIER) cc_final: 0.0243 (mt) REVERT: C 262 PHE cc_start: 0.6567 (t80) cc_final: 0.5966 (t80) REVERT: D 105 TRP cc_start: 0.6546 (m100) cc_final: 0.5770 (m100) REVERT: E 16 VAL cc_start: 0.8502 (t) cc_final: 0.8155 (m) REVERT: E 39 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: E 88 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8458 (mmtt) REVERT: G 49 ARG cc_start: 0.8750 (ttt180) cc_final: 0.8506 (ttt180) REVERT: H 29 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: H 75 GLU cc_start: 0.6759 (tt0) cc_final: 0.6249 (mm-30) REVERT: H 88 LYS cc_start: 0.8460 (mmmt) cc_final: 0.7773 (tttm) REVERT: I 28 GLU cc_start: 0.7634 (tt0) cc_final: 0.7314 (tm-30) REVERT: I 183 MET cc_start: 0.5396 (ptm) cc_final: 0.4676 (mpp) REVERT: I 205 VAL cc_start: 0.6556 (t) cc_final: 0.6265 (t) REVERT: I 230 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5893 (pp20) REVERT: I 288 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8031 (mp0) REVERT: I 293 ILE cc_start: 0.5198 (tp) cc_final: 0.4855 (mt) REVERT: I 328 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7505 (tp) REVERT: J 26 TYR cc_start: 0.7198 (t80) cc_final: 0.6897 (t80) REVERT: J 92 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6052 (pp20) REVERT: J 124 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8073 (tp) REVERT: K 77 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8413 (p) REVERT: K 104 GLN cc_start: 0.8514 (pm20) cc_final: 0.8216 (mm110) REVERT: K 155 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7192 (tpt170) REVERT: K 293 ILE cc_start: 0.9304 (tt) cc_final: 0.9089 (tt) REVERT: L 1 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6619 (ttm) REVERT: L 81 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8598 (mt) REVERT: L 217 GLU cc_start: 0.8122 (tp30) cc_final: 0.7741 (pt0) REVERT: M 245 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8377 (tpp) REVERT: N 183 MET cc_start: 0.7983 (ppp) cc_final: 0.6996 (ppp) REVERT: O 1 MET cc_start: 0.6648 (tpp) cc_final: 0.6331 (tpt) REVERT: O 201 ASP cc_start: 0.7625 (t0) cc_final: 0.7349 (t0) REVERT: O 304 ILE cc_start: 0.8665 (mp) cc_final: 0.8398 (mt) REVERT: O 335 MET cc_start: 0.8361 (tmm) cc_final: 0.7918 (ttm) REVERT: P 167 LYS cc_start: 0.6103 (mptt) cc_final: 0.5769 (mttp) outliers start: 67 outliers final: 46 residues processed: 311 average time/residue: 0.3818 time to fit residues: 192.3786 Evaluate side-chains 293 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 155 LEU 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 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 29 ASP 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 64 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 328 LEU 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 278 LEU 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 77 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 215 PHE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 237 SER 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 245 MET Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 293 ILE 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 86 THR Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 286 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 328 optimal weight: 0.2980 chunk 70 optimal weight: 0.2980 chunk 312 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 chunk 287 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.139506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099319 restraints weight = 61191.537| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.27 r_work: 0.3367 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.8251 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= 0.129 Angle : 0.637 14.479 38281 Z= 0.322 Chirality : 0.044 0.358 4389 Planarity : 0.004 0.066 4745 Dihedral : 12.169 178.367 4355 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.12 % Favored : 92.82 % Rotamer: Outliers : 2.06 % Allowed : 23.86 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3341 helix: 0.47 (0.16), residues: 1181 sheet: -0.08 (0.22), residues: 566 loop : -1.70 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP J 42 HIS 0.004 0.001 HIS L 59 PHE 0.018 0.001 PHE C 273 TYR 0.029 0.001 TYR J 2 ARG 0.014 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.02801 ( 867) hydrogen bonds : angle 4.29105 ( 2478) SS BOND : bond 0.00138 ( 5) SS BOND : angle 1.19693 ( 10) covalent geometry : bond 0.00297 (28088) covalent geometry : angle 0.63680 (38271) ********************** 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 313 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 255 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LEU cc_start: 0.6512 (tp) cc_final: 0.6276 (tt) REVERT: C 111 MET cc_start: -0.0760 (mmm) cc_final: -0.1178 (ptt) REVERT: C 155 LEU cc_start: 0.0545 (OUTLIER) cc_final: 0.0242 (mt) REVERT: C 262 PHE cc_start: 0.6630 (t80) cc_final: 0.6131 (t80) REVERT: D 105 TRP cc_start: 0.6508 (m100) cc_final: 0.5777 (m100) REVERT: E 16 VAL cc_start: 0.8546 (t) cc_final: 0.8231 (m) REVERT: E 88 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8539 (mmtt) REVERT: G 49 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8277 (ttt180) REVERT: H 29 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: H 75 GLU cc_start: 0.6785 (tt0) cc_final: 0.6266 (mm-30) REVERT: H 88 LYS cc_start: 0.8456 (mmmt) cc_final: 0.7783 (tttm) REVERT: I 183 MET cc_start: 0.5495 (ptm) cc_final: 0.4787 (mpp) REVERT: I 205 VAL cc_start: 0.6786 (t) cc_final: 0.6513 (t) REVERT: I 230 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5871 (pp20) REVERT: I 288 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7980 (mp0) REVERT: I 293 ILE cc_start: 0.5404 (tp) cc_final: 0.5050 (mt) REVERT: J 26 TYR cc_start: 0.7052 (t80) cc_final: 0.6833 (t80) REVERT: J 54 MET cc_start: 0.8598 (tpt) cc_final: 0.8393 (tpt) REVERT: J 92 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.5929 (pp20) REVERT: J 124 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8000 (tp) REVERT: K 155 ARG cc_start: 0.7613 (mtt-85) cc_final: 0.7227 (tpt170) REVERT: K 293 ILE cc_start: 0.9238 (tt) cc_final: 0.8968 (tt) REVERT: L 1 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6576 (ttm) REVERT: L 81 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8553 (mt) REVERT: M 245 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8090 (ttm) REVERT: N 183 MET cc_start: 0.7983 (ppp) cc_final: 0.7058 (ppp) REVERT: O 1 MET cc_start: 0.6596 (tpp) cc_final: 0.6279 (tpt) REVERT: O 201 ASP cc_start: 0.7484 (t0) cc_final: 0.7218 (t0) REVERT: O 209 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: O 304 ILE cc_start: 0.8625 (mp) cc_final: 0.8344 (mt) REVERT: O 335 MET cc_start: 0.8273 (tmm) cc_final: 0.7808 (ttm) REVERT: P 98 GLU cc_start: 0.2036 (pm20) cc_final: 0.1703 (pm20) REVERT: P 141 MET cc_start: 0.3392 (tmm) cc_final: 0.3175 (tmm) REVERT: P 167 LYS cc_start: 0.6061 (mptt) cc_final: 0.5724 (mttp) outliers start: 58 outliers final: 46 residues processed: 301 average time/residue: 0.3761 time to fit residues: 183.1385 Evaluate side-chains 294 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 63 SER 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 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 29 ASP Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 47 VAL 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 328 LEU 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 278 LEU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 215 PHE 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 L residue 1 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 245 MET Chi-restraints excluded: chain N residue 219 GLN Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 293 ILE 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 86 THR Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 209 GLN Chi-restraints excluded: chain O residue 286 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 16 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 300 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 28 optimal weight: 0.0000 chunk 8 optimal weight: 30.0000 chunk 92 optimal weight: 0.0000 chunk 134 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 329 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.139486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101220 restraints weight = 62237.013| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.62 r_work: 0.3365 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.8356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28093 Z= 0.119 Angle : 0.632 14.427 38281 Z= 0.316 Chirality : 0.044 0.334 4389 Planarity : 0.005 0.058 4745 Dihedral : 12.148 178.070 4355 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.52 % Favored : 93.42 % Rotamer: Outliers : 2.06 % Allowed : 24.03 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 3341 helix: 0.50 (0.16), residues: 1180 sheet: -0.11 (0.22), residues: 578 loop : -1.65 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 42 HIS 0.004 0.001 HIS N 121 PHE 0.030 0.001 PHE P 89 TYR 0.027 0.001 TYR I 309 ARG 0.015 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 867) hydrogen bonds : angle 4.26803 ( 2478) SS BOND : bond 0.00140 ( 5) SS BOND : angle 1.08253 ( 10) covalent geometry : bond 0.00268 (28088) covalent geometry : angle 0.63196 (38271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15621.11 seconds wall clock time: 273 minutes 22.66 seconds (16402.66 seconds total)