Starting phenix.real_space_refine on Tue Feb 20 09:21:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/02_2024/7tr6_26081_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/02_2024/7tr6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/02_2024/7tr6_26081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/02_2024/7tr6_26081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/02_2024/7tr6_26081_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/02_2024/7tr6_26081_neut.pdb" } 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 Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "G TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 26": "OD1" <-> "OD2" Residue "I TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 284": "OE1" <-> "OE2" Residue "J PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 284": "OE1" <-> "OE2" Residue "K PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 284": "OE1" <-> "OE2" Residue "N ASP 312": "OD1" <-> "OD2" Residue "P PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 14.25, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 10.99 Conformation dependent library (CDL) restraints added in 4.9 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: 8.71 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: 8.51 Time building geometry restraints manager: 11.86 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: 98.25 - 105.41: 713 105.41 - 112.57: 14790 112.57 - 119.73: 9275 119.73 - 126.89: 13099 126.89 - 134.05: 394 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 2.440 nonbonded pdb=" NH1 ARG P 110 " pdb=" OE1 GLU P 112 " model vdw 2.148 2.520 nonbonded pdb=" OD1 ASP K 65 " pdb=" OH TYR K 83 " model vdw 2.164 2.440 nonbonded pdb=" O ASN J 253 " pdb=" OG SER J 257 " model vdw 2.167 2.440 nonbonded pdb=" O2' A R 1 " pdb=" OP2 U R 2 " model vdw 2.188 2.440 ... (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 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: 3.660 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: 13.190 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 75.720 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.130 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.510 ------------------------------------------------------------------------------- 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 28088 Z= 0.183 Angle : 0.574 10.007 38271 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 741 time to evaluate : 3.091 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: 0.4303 time to fit residues: 485.2210 Evaluate side-chains 363 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 3.234 ------------------------------------------------------------------------------- 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: 5.9990 chunk 86 optimal weight: 3.9990 chunk 171 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 304 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS C 165 HIS C 182 HIS I 17 ASN I 57 HIS I 182 GLN K 17 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 310 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28088 Z= 0.326 Angle : 0.774 17.820 38271 Z= 0.390 Chirality : 0.049 0.346 4389 Planarity : 0.006 0.079 4745 Dihedral : 12.160 175.583 4355 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.36 % Favored : 92.61 % Rotamer: Outliers : 2.98 % Allowed : 13.31 % Favored : 83.71 % 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: -1.26 (0.14), residues: 3341 helix: -0.02 (0.15), residues: 1147 sheet: -0.19 (0.23), residues: 534 loop : -1.65 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP F 4 HIS 0.012 0.002 HIS L 57 PHE 0.032 0.003 PHE C 288 TYR 0.031 0.003 TYR C 99 ARG 0.021 0.001 ARG E 10 *********************** 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 490 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 406 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 SER cc_start: 0.5706 (m) cc_final: 0.5132 (p) REVERT: C 111 MET cc_start: 0.0610 (mmm) cc_final: 0.0010 (ptt) REVERT: C 191 GLU cc_start: 0.6394 (mm-30) cc_final: 0.5980 (mt-10) REVERT: C 262 PHE cc_start: 0.5896 (t80) cc_final: 0.5540 (t80) REVERT: C 283 TYR cc_start: 0.5452 (t80) cc_final: 0.4911 (p90) REVERT: D 5 ILE cc_start: 0.3052 (OUTLIER) cc_final: 0.2820 (tp) REVERT: E 29 ASP cc_start: 0.7989 (m-30) cc_final: 0.7609 (p0) REVERT: H 72 GLU cc_start: 0.8435 (tp30) cc_final: 0.7879 (mp0) REVERT: H 75 GLU cc_start: 0.6574 (tt0) cc_final: 0.6188 (mm-30) REVERT: H 88 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7339 (ptmm) REVERT: I 58 TRP cc_start: 0.6042 (m100) cc_final: 0.5666 (m100) REVERT: I 108 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7277 (tt0) REVERT: I 183 MET cc_start: 0.3898 (ptm) cc_final: 0.3683 (ptp) REVERT: I 288 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7731 (mp0) REVERT: I 293 ILE cc_start: 0.3925 (tp) cc_final: 0.3541 (mt) REVERT: J 1 MET cc_start: 0.7330 (mmm) cc_final: 0.7021 (tpp) REVERT: J 2 TYR cc_start: 0.7891 (m-80) cc_final: 0.7591 (m-80) REVERT: J 53 ASN cc_start: 0.7519 (t0) cc_final: 0.7120 (t0) REVERT: J 194 TYR cc_start: 0.7627 (m-80) cc_final: 0.7333 (m-10) REVERT: J 316 ASP cc_start: 0.8449 (m-30) cc_final: 0.7889 (p0) REVERT: K 183 MET cc_start: 0.5762 (pmm) cc_final: 0.5465 (pmm) REVERT: K 293 ILE cc_start: 0.9205 (tt) cc_final: 0.9004 (tp) REVERT: L 214 LYS cc_start: 0.8533 (tppt) cc_final: 0.7156 (pttm) REVERT: L 285 ASP cc_start: 0.8133 (t0) cc_final: 0.7882 (t0) REVERT: M 96 THR cc_start: 0.8902 (m) cc_final: 0.8550 (p) REVERT: M 326 GLU cc_start: 0.7280 (pm20) cc_final: 0.6818 (pm20) REVERT: O 10 ARG cc_start: 0.7144 (ttm170) cc_final: 0.5161 (ptt90) REVERT: O 67 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6795 (t80) REVERT: O 82 ARG cc_start: 0.6613 (ptp90) cc_final: 0.5291 (mmt180) REVERT: O 104 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: O 105 LEU cc_start: 0.7515 (mp) cc_final: 0.7269 (mt) REVERT: O 211 LEU cc_start: 0.7201 (tp) cc_final: 0.6770 (mp) REVERT: P 98 GLU cc_start: 0.1926 (pm20) cc_final: -0.0262 (tm-30) REVERT: P 216 ILE cc_start: 0.6405 (mp) cc_final: 0.6105 (tt) REVERT: P 242 LYS cc_start: 0.5222 (tptp) cc_final: 0.4316 (pttp) outliers start: 84 outliers final: 41 residues processed: 473 average time/residue: 0.4354 time to fit residues: 324.7170 Evaluate side-chains 333 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 289 time to evaluate : 2.946 ------------------------------------------------------------------------------- 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 53 LYS Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 16 VAL 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 321 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain 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 110 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 316 ASP 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 36 VAL Chi-restraints excluded: chain N residue 198 ILE Chi-restraints excluded: chain N residue 239 LEU Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain O residue 226 ILE Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain P residue 156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 253 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 329 optimal weight: 20.0000 chunk 271 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 17 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN L 229 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN N 25 ASN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 14 HIS ** O 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28088 Z= 0.275 Angle : 0.653 12.578 38271 Z= 0.331 Chirality : 0.046 0.203 4389 Planarity : 0.005 0.107 4745 Dihedral : 12.101 176.808 4355 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 3.05 % Allowed : 18.14 % Favored : 78.81 % 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: -1.17 (0.14), residues: 3341 helix: 0.02 (0.15), residues: 1209 sheet: -0.06 (0.23), residues: 533 loop : -1.66 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 105 HIS 0.008 0.002 HIS L 162 PHE 0.023 0.002 PHE J 261 TYR 0.023 0.002 TYR H 14 ARG 0.012 0.001 ARG F 10 *********************** 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 400 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 314 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 SER cc_start: 0.5671 (m) cc_final: 0.5099 (p) REVERT: C 111 MET cc_start: 0.0383 (mmm) cc_final: -0.0233 (ptt) REVERT: C 226 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.5958 (pp) REVERT: C 259 ILE cc_start: 0.3442 (mt) cc_final: 0.3222 (tt) REVERT: C 262 PHE cc_start: 0.6172 (t80) cc_final: 0.5605 (t80) REVERT: C 283 TYR cc_start: 0.5240 (t80) cc_final: 0.4822 (p90) REVERT: D 105 TRP cc_start: 0.5876 (m100) cc_final: 0.5037 (m100) REVERT: E 29 ASP cc_start: 0.8002 (m-30) cc_final: 0.7446 (p0) REVERT: G 14 TYR cc_start: 0.8005 (m-80) cc_final: 0.7799 (m-80) REVERT: G 70 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7923 (p) REVERT: I 108 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7727 (tt0) REVERT: I 288 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7772 (mp0) REVERT: I 293 ILE cc_start: 0.4321 (tp) cc_final: 0.3877 (mt) REVERT: J 253 ASN cc_start: 0.8932 (t0) cc_final: 0.8712 (t0) REVERT: K 135 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8883 (mp) REVERT: K 293 ILE cc_start: 0.9371 (tt) cc_final: 0.9125 (tp) REVERT: M 54 MET cc_start: 0.8120 (tpp) cc_final: 0.7707 (tpp) REVERT: M 96 THR cc_start: 0.8887 (m) cc_final: 0.8524 (p) REVERT: M 224 ILE cc_start: 0.8797 (mm) cc_final: 0.8596 (mm) REVERT: M 326 GLU cc_start: 0.7203 (pm20) cc_final: 0.6765 (pm20) REVERT: M 335 MET cc_start: 0.8840 (ptm) cc_final: 0.8631 (ptt) REVERT: N 130 ARG cc_start: 0.7240 (mmp80) cc_final: 0.6607 (mmp80) REVERT: N 227 ASP cc_start: 0.7684 (t0) cc_final: 0.7386 (t0) REVERT: O 10 ARG cc_start: 0.7440 (ttm170) cc_final: 0.5129 (ptt90) REVERT: O 67 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6540 (t80) REVERT: O 82 ARG cc_start: 0.6967 (ptp90) cc_final: 0.5446 (mmt180) REVERT: O 201 ASP cc_start: 0.6704 (t0) cc_final: 0.6366 (t0) REVERT: O 245 MET cc_start: 0.6873 (mtp) cc_final: 0.6441 (ttm) REVERT: P 98 GLU cc_start: 0.1549 (pm20) cc_final: -0.0370 (tm-30) REVERT: P 242 LYS cc_start: 0.5197 (tptp) cc_final: 0.4278 (pttm) outliers start: 86 outliers final: 47 residues processed: 383 average time/residue: 0.4106 time to fit residues: 252.8169 Evaluate side-chains 311 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 260 time to evaluate : 3.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 228 HIS 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 96 SER 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 82 GLU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 321 LYS Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 139 SER 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 313 LEU 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 135 LEU Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 215 PHE 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 239 LEU Chi-restraints excluded: chain M residue 249 TYR 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 70 THR Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 65 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 2.9990 chunk 229 optimal weight: 0.6980 chunk 158 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 323 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 289 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN K 53 ASN ** L 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28088 Z= 0.187 Angle : 0.589 13.502 38271 Z= 0.297 Chirality : 0.043 0.197 4389 Planarity : 0.004 0.060 4745 Dihedral : 12.010 177.859 4355 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.91 % Favored : 93.03 % Rotamer: Outliers : 2.59 % Allowed : 20.20 % Favored : 77.21 % 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: -1.06 (0.15), residues: 3341 helix: 0.15 (0.15), residues: 1215 sheet: 0.01 (0.23), residues: 527 loop : -1.64 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 105 HIS 0.005 0.001 HIS L 57 PHE 0.022 0.001 PHE J 261 TYR 0.012 0.001 TYR C 157 ARG 0.009 0.000 ARG F 35 *********************** 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 361 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 288 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 SER cc_start: 0.5855 (m) cc_final: 0.5587 (p) REVERT: C 94 ASN cc_start: 0.1226 (OUTLIER) cc_final: 0.0767 (t0) REVERT: C 259 ILE cc_start: 0.3415 (mt) cc_final: 0.3204 (tt) REVERT: C 262 PHE cc_start: 0.6228 (t80) cc_final: 0.5587 (t80) REVERT: D 105 TRP cc_start: 0.5990 (m100) cc_final: 0.5696 (m100) REVERT: E 29 ASP cc_start: 0.7863 (m-30) cc_final: 0.7436 (p0) REVERT: E 79 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7200 (mm-30) REVERT: G 70 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7822 (p) REVERT: H 22 GLU cc_start: 0.7632 (tp30) cc_final: 0.7352 (tp30) REVERT: I 108 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7783 (tt0) REVERT: I 265 GLU cc_start: 0.4622 (tt0) cc_final: 0.4183 (tt0) REVERT: I 288 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7744 (mp0) REVERT: I 293 ILE cc_start: 0.4361 (tp) cc_final: 0.3879 (mt) REVERT: J 253 ASN cc_start: 0.8835 (t0) cc_final: 0.8605 (t0) REVERT: J 316 ASP cc_start: 0.8347 (m-30) cc_final: 0.7925 (p0) REVERT: K 202 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8304 (pp) REVERT: L 285 ASP cc_start: 0.8300 (t0) cc_final: 0.8019 (t0) REVERT: M 54 MET cc_start: 0.7949 (tpp) cc_final: 0.7608 (tpp) REVERT: M 96 THR cc_start: 0.8914 (m) cc_final: 0.8585 (p) REVERT: N 130 ARG cc_start: 0.7350 (mmp80) cc_final: 0.6580 (mmp80) REVERT: N 227 ASP cc_start: 0.7769 (t0) cc_final: 0.7449 (t0) REVERT: O 10 ARG cc_start: 0.7498 (ttm170) cc_final: 0.4920 (ptt90) REVERT: O 67 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6743 (t80) REVERT: O 82 ARG cc_start: 0.6893 (ptp90) cc_final: 0.5604 (mmt180) REVERT: O 201 ASP cc_start: 0.6805 (t0) cc_final: 0.6495 (t0) REVERT: O 245 MET cc_start: 0.6869 (mtp) cc_final: 0.6500 (ttm) REVERT: O 265 GLU cc_start: 0.7187 (tt0) cc_final: 0.6940 (tt0) REVERT: P 98 GLU cc_start: 0.1260 (pm20) cc_final: -0.0619 (tm-30) REVERT: P 242 LYS cc_start: 0.5257 (tptp) cc_final: 0.4346 (pttm) outliers start: 73 outliers final: 41 residues processed: 347 average time/residue: 0.3770 time to fit residues: 212.6160 Evaluate side-chains 310 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 265 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 228 HIS 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 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 82 GLU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 321 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 286 TYR Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain P residue 65 GLU 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 269 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 241 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 276 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 290 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 HIS ** L 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.6955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 28088 Z= 0.291 Angle : 0.651 13.444 38271 Z= 0.333 Chirality : 0.046 0.243 4389 Planarity : 0.005 0.101 4745 Dihedral : 12.095 178.018 4355 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 4.26 % Allowed : 20.13 % Favored : 75.61 % 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 (0.14), residues: 3341 helix: 0.22 (0.15), residues: 1193 sheet: -0.21 (0.22), residues: 554 loop : -1.74 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 100 HIS 0.010 0.002 HIS L 162 PHE 0.030 0.002 PHE I 88 TYR 0.024 0.002 TYR G 14 ARG 0.012 0.001 ARG K 221 *********************** 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 fitting. rotamer outliers: 120 poor density : 295 time to evaluate : 3.176 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: C 63 SER cc_start: 0.5879 (m) cc_final: 0.5244 (p) REVERT: C 94 ASN cc_start: 0.1585 (OUTLIER) cc_final: 0.1103 (t0) REVERT: C 111 MET cc_start: 0.0515 (mmm) cc_final: -0.0235 (ptt) REVERT: C 259 ILE cc_start: 0.3310 (mt) cc_final: 0.3061 (tt) REVERT: C 262 PHE cc_start: 0.6382 (t80) cc_final: 0.5627 (t80) REVERT: C 271 MET cc_start: -0.0917 (OUTLIER) cc_final: -0.1327 (mmm) REVERT: D 105 TRP cc_start: 0.6064 (m100) cc_final: 0.5728 (m100) REVERT: E 29 ASP cc_start: 0.7819 (m-30) cc_final: 0.7269 (p0) REVERT: E 88 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8407 (mmtt) REVERT: G 70 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8290 (p) REVERT: H 13 SER cc_start: 0.7776 (t) cc_final: 0.7505 (p) REVERT: H 57 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6236 (ttpp) REVERT: I 12 ASN cc_start: 0.6717 (OUTLIER) cc_final: 0.5866 (p0) REVERT: I 108 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7724 (tt0) REVERT: I 132 ARG cc_start: 0.0596 (ttt90) cc_final: 0.0351 (ttt-90) REVERT: I 230 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5805 (pp20) REVERT: I 253 ASN cc_start: 0.8236 (t0) cc_final: 0.7940 (t0) REVERT: I 293 ILE cc_start: 0.4547 (tp) cc_final: 0.4179 (mt) REVERT: J 253 ASN cc_start: 0.8944 (t0) cc_final: 0.8664 (t0) REVERT: J 316 ASP cc_start: 0.8374 (m-30) cc_final: 0.7905 (p0) REVERT: K 202 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8585 (pp) REVERT: K 293 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8979 (tp) REVERT: L 1 MET cc_start: 0.6405 (ttm) cc_final: 0.6019 (ttt) REVERT: L 81 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8701 (mt) REVERT: M 54 MET cc_start: 0.8161 (tpp) cc_final: 0.7566 (tpp) REVERT: M 326 GLU cc_start: 0.7240 (pm20) cc_final: 0.6911 (pm20) REVERT: N 227 ASP cc_start: 0.8059 (t0) cc_final: 0.7850 (t0) REVERT: O 1 MET cc_start: 0.6916 (tpp) cc_final: 0.6352 (tpt) REVERT: O 30 THR cc_start: 0.7280 (p) cc_final: 0.6999 (t) REVERT: O 201 ASP cc_start: 0.7236 (t0) cc_final: 0.7034 (t0) REVERT: O 245 MET cc_start: 0.7069 (mtp) cc_final: 0.6765 (ttm) REVERT: O 265 GLU cc_start: 0.7698 (tt0) cc_final: 0.7217 (tt0) REVERT: P 167 LYS cc_start: 0.6097 (mptt) cc_final: 0.5825 (mttp) outliers start: 120 outliers final: 66 residues processed: 396 average time/residue: 0.3702 time to fit residues: 237.3523 Evaluate side-chains 317 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 242 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ASN 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 271 MET 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 F residue 108 CYS Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 321 LYS Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 70 THR 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 K residue 6 SER Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 215 PHE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 293 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 5 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 45 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 198 ILE Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 40 ASN 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 134 SER Chi-restraints excluded: chain O residue 196 PHE Chi-restraints excluded: chain O residue 226 ILE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 4.9990 chunk 291 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 324 optimal weight: 9.9990 chunk 269 optimal weight: 0.4980 chunk 150 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.7375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28088 Z= 0.250 Angle : 0.612 13.573 38271 Z= 0.312 Chirality : 0.045 0.236 4389 Planarity : 0.004 0.062 4745 Dihedral : 12.038 179.971 4355 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.09 % Favored : 92.85 % Rotamer: Outliers : 3.30 % Allowed : 22.22 % Favored : 74.48 % 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: 0.21 (0.15), residues: 1230 sheet: -0.10 (0.22), residues: 558 loop : -1.68 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 100 HIS 0.006 0.001 HIS L 162 PHE 0.022 0.002 PHE P 89 TYR 0.016 0.001 TYR J 26 ARG 0.011 0.000 ARG F 35 *********************** 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 360 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 267 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LEU cc_start: 0.6252 (tp) cc_final: 0.5974 (tt) REVERT: C 63 SER cc_start: 0.5743 (m) cc_final: 0.5137 (p) REVERT: C 94 ASN cc_start: 0.1248 (OUTLIER) cc_final: 0.1013 (t0) REVERT: C 111 MET cc_start: 0.0372 (mmm) cc_final: -0.0530 (ptt) REVERT: C 191 GLU cc_start: 0.4938 (mt-10) cc_final: 0.4480 (pt0) REVERT: C 259 ILE cc_start: 0.3383 (mt) cc_final: 0.3106 (tt) REVERT: C 262 PHE cc_start: 0.6379 (t80) cc_final: 0.5884 (t80) REVERT: C 271 MET cc_start: -0.1055 (OUTLIER) cc_final: -0.1343 (mmm) REVERT: D 37 GLN cc_start: 0.6497 (OUTLIER) cc_final: 0.5728 (tp40) REVERT: D 48 LEU cc_start: 0.8801 (mt) cc_final: 0.8595 (tp) REVERT: D 105 TRP cc_start: 0.6080 (m100) cc_final: 0.5022 (m100) REVERT: E 16 VAL cc_start: 0.8163 (t) cc_final: 0.7919 (m) REVERT: E 29 ASP cc_start: 0.7778 (m-30) cc_final: 0.7246 (p0) REVERT: G 70 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8348 (p) REVERT: H 13 SER cc_start: 0.8040 (t) cc_final: 0.7777 (p) REVERT: H 57 LYS cc_start: 0.6916 (ptmm) cc_final: 0.6249 (ttpp) REVERT: H 88 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7830 (ptmm) REVERT: I 108 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7800 (tt0) REVERT: I 213 VAL cc_start: 0.6514 (OUTLIER) cc_final: 0.6168 (p) REVERT: I 230 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5923 (pp20) REVERT: I 253 ASN cc_start: 0.8318 (t0) cc_final: 0.8047 (t0) REVERT: I 293 ILE cc_start: 0.5022 (tp) cc_final: 0.4619 (mt) REVERT: J 316 ASP cc_start: 0.8298 (m-30) cc_final: 0.7934 (p0) REVERT: K 77 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8464 (p) REVERT: K 202 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8577 (pp) REVERT: K 293 ILE cc_start: 0.9411 (tt) cc_final: 0.9054 (tt) REVERT: L 1 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5992 (ttt) REVERT: L 81 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8684 (mt) REVERT: L 217 GLU cc_start: 0.7808 (tp30) cc_final: 0.7180 (pt0) REVERT: M 54 MET cc_start: 0.8051 (tpp) cc_final: 0.7128 (tpp) REVERT: M 162 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.7848 (p90) REVERT: N 335 MET cc_start: 0.8830 (ttp) cc_final: 0.8542 (ttp) REVERT: O 1 MET cc_start: 0.6892 (tpp) cc_final: 0.6259 (tpt) REVERT: O 201 ASP cc_start: 0.7260 (t0) cc_final: 0.6995 (t0) REVERT: O 265 GLU cc_start: 0.7814 (tt0) cc_final: 0.7314 (tt0) REVERT: O 335 MET cc_start: 0.8775 (tmm) cc_final: 0.8467 (tmm) REVERT: P 167 LYS cc_start: 0.6198 (mptt) cc_final: 0.5904 (mtmt) outliers start: 93 outliers final: 59 residues processed: 344 average time/residue: 0.3708 time to fit residues: 205.4821 Evaluate side-chains 312 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 242 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain 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 G residue 70 SER Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 82 GLU 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 111 ILE Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 321 LYS Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 86 THR 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 202 LEU Chi-restraints excluded: chain K residue 215 PHE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 1 MET 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 17 ASN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 162 HIS Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 40 ASN 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 134 SER Chi-restraints excluded: chain O residue 226 ILE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain O residue 324 SER Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 164 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 272 optimal weight: 0.6980 chunk 180 optimal weight: 0.7980 chunk 322 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN J 310 ASN L 182 GLN ** L 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 HIS ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.7553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28088 Z= 0.187 Angle : 0.599 14.749 38271 Z= 0.301 Chirality : 0.044 0.385 4389 Planarity : 0.004 0.062 4745 Dihedral : 11.991 179.317 4355 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.67 % Favored : 93.27 % Rotamer: Outliers : 3.05 % Allowed : 23.07 % Favored : 73.87 % 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: -0.96 (0.15), residues: 3341 helix: 0.39 (0.15), residues: 1203 sheet: -0.08 (0.22), residues: 581 loop : -1.69 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 105 HIS 0.004 0.001 HIS L 57 PHE 0.025 0.001 PHE C 288 TYR 0.014 0.001 TYR M 72 ARG 0.012 0.000 ARG F 35 *********************** 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 347 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 261 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LEU cc_start: 0.6292 (tp) cc_final: 0.6009 (tt) REVERT: C 63 SER cc_start: 0.5614 (m) cc_final: 0.4997 (p) REVERT: C 94 ASN cc_start: 0.1257 (OUTLIER) cc_final: 0.0987 (t0) REVERT: C 111 MET cc_start: 0.0273 (mmm) cc_final: -0.0521 (ptt) REVERT: C 155 LEU cc_start: 0.0715 (OUTLIER) cc_final: 0.0490 (mt) REVERT: C 191 GLU cc_start: 0.4982 (mt-10) cc_final: 0.4525 (pt0) REVERT: C 259 ILE cc_start: 0.3346 (mt) cc_final: 0.3073 (tt) REVERT: C 262 PHE cc_start: 0.6444 (t80) cc_final: 0.5829 (t80) REVERT: C 271 MET cc_start: -0.0973 (OUTLIER) cc_final: -0.1249 (mmm) REVERT: D 37 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.5733 (tp40) REVERT: D 48 LEU cc_start: 0.8671 (mt) cc_final: 0.8461 (tp) REVERT: D 105 TRP cc_start: 0.5861 (m100) cc_final: 0.5373 (m100) REVERT: E 16 VAL cc_start: 0.8199 (t) cc_final: 0.7983 (m) REVERT: E 29 ASP cc_start: 0.7701 (m-30) cc_final: 0.7297 (p0) REVERT: E 88 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8428 (mmtt) REVERT: G 70 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8342 (p) REVERT: H 57 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6287 (ttpp) REVERT: H 88 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7867 (ptmm) REVERT: I 108 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7712 (tt0) REVERT: I 213 VAL cc_start: 0.6544 (m) cc_final: 0.6197 (p) REVERT: I 230 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5897 (pp20) REVERT: I 293 ILE cc_start: 0.5264 (tp) cc_final: 0.4860 (mt) REVERT: J 54 MET cc_start: 0.9004 (tpp) cc_final: 0.8563 (tpp) REVERT: J 245 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.5985 (mtp) REVERT: J 316 ASP cc_start: 0.8290 (m-30) cc_final: 0.7908 (p0) REVERT: K 77 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8459 (p) REVERT: K 155 ARG cc_start: 0.7487 (mtt-85) cc_final: 0.6778 (tpt170) REVERT: K 202 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8534 (pp) REVERT: K 293 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8992 (tp) REVERT: L 1 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.6142 (ttm) REVERT: L 81 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8634 (mt) REVERT: M 54 MET cc_start: 0.8025 (tpp) cc_final: 0.7158 (tpp) REVERT: N 117 ASP cc_start: 0.7747 (m-30) cc_final: 0.7515 (m-30) REVERT: N 335 MET cc_start: 0.8733 (ttp) cc_final: 0.8455 (ttp) REVERT: O 1 MET cc_start: 0.6857 (tpp) cc_final: 0.6344 (tpt) REVERT: O 201 ASP cc_start: 0.7223 (t0) cc_final: 0.6952 (t0) REVERT: O 265 GLU cc_start: 0.7828 (tt0) cc_final: 0.7362 (tt0) REVERT: O 335 MET cc_start: 0.8720 (tmm) cc_final: 0.8393 (tmm) REVERT: P 164 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.5293 (mp0) REVERT: P 167 LYS cc_start: 0.6195 (mptt) cc_final: 0.5917 (mtmt) outliers start: 86 outliers final: 59 residues processed: 329 average time/residue: 0.3740 time to fit residues: 199.7746 Evaluate side-chains 317 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 244 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ASN 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 271 MET 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 37 GLN 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 G residue 70 SER Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 245 MET 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 202 LEU 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 K residue 316 ASP Chi-restraints excluded: chain L residue 1 MET 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 M residue 239 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 226 ILE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain O residue 324 SER Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 109 MET Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 164 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 219 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 HIS ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.8023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28088 Z= 0.253 Angle : 0.631 13.726 38271 Z= 0.321 Chirality : 0.045 0.422 4389 Planarity : 0.005 0.129 4745 Dihedral : 11.977 179.782 4355 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.21 % Favored : 92.73 % Rotamer: Outliers : 3.27 % Allowed : 23.18 % Favored : 73.55 % 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: 0.40 (0.16), residues: 1199 sheet: -0.15 (0.22), residues: 582 loop : -1.71 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 100 HIS 0.007 0.001 HIS K 57 PHE 0.032 0.002 PHE C 288 TYR 0.016 0.001 TYR D 14 ARG 0.014 0.000 ARG F 35 *********************** 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 354 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 262 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LEU cc_start: 0.6316 (tp) cc_final: 0.6078 (tt) REVERT: C 63 SER cc_start: 0.5583 (m) cc_final: 0.4993 (p) REVERT: C 94 ASN cc_start: 0.1260 (OUTLIER) cc_final: 0.1029 (t0) REVERT: C 111 MET cc_start: 0.0008 (mmm) cc_final: -0.0768 (ptt) REVERT: C 155 LEU cc_start: 0.0574 (OUTLIER) cc_final: 0.0295 (mt) REVERT: C 175 LYS cc_start: 0.2516 (tmtt) cc_final: 0.2292 (pptt) REVERT: C 177 ASP cc_start: 0.2015 (OUTLIER) cc_final: 0.1789 (p0) REVERT: C 191 GLU cc_start: 0.5026 (OUTLIER) cc_final: 0.4577 (pt0) REVERT: C 259 ILE cc_start: 0.3287 (mt) cc_final: 0.3009 (tt) REVERT: C 262 PHE cc_start: 0.6327 (t80) cc_final: 0.5872 (t80) REVERT: C 271 MET cc_start: -0.1018 (OUTLIER) cc_final: -0.1242 (mmm) REVERT: D 37 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.5995 (tp40) REVERT: D 105 TRP cc_start: 0.6202 (m100) cc_final: 0.5556 (m100) REVERT: E 29 ASP cc_start: 0.7851 (m-30) cc_final: 0.7240 (p0) REVERT: E 88 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8536 (mmtt) REVERT: G 70 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8267 (p) REVERT: H 29 ASP cc_start: 0.8703 (t0) cc_final: 0.8404 (m-30) REVERT: H 57 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6667 (ttpp) REVERT: H 75 GLU cc_start: 0.6756 (tt0) cc_final: 0.6143 (mm-30) REVERT: H 79 GLU cc_start: 0.8204 (pm20) cc_final: 0.7095 (mm-30) REVERT: H 88 LYS cc_start: 0.8477 (mmmt) cc_final: 0.7980 (ptmm) REVERT: I 28 GLU cc_start: 0.7034 (tt0) cc_final: 0.6558 (tm-30) REVERT: I 108 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7806 (tt0) REVERT: I 205 VAL cc_start: 0.6645 (t) cc_final: 0.6371 (t) REVERT: I 213 VAL cc_start: 0.6606 (m) cc_final: 0.6246 (p) REVERT: I 230 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6052 (pp20) REVERT: I 276 PRO cc_start: 0.4020 (Cg_endo) cc_final: 0.3597 (Cg_exo) REVERT: I 288 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7995 (mp0) REVERT: I 293 ILE cc_start: 0.5280 (tp) cc_final: 0.4916 (mt) REVERT: J 54 MET cc_start: 0.8994 (tpp) cc_final: 0.8381 (tpp) REVERT: J 245 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6219 (mtp) REVERT: J 316 ASP cc_start: 0.8251 (m-30) cc_final: 0.7884 (p0) REVERT: K 77 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8350 (p) REVERT: K 155 ARG cc_start: 0.7628 (mtt-85) cc_final: 0.7062 (tpt170) REVERT: K 202 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8612 (pp) REVERT: K 293 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9003 (tt) REVERT: L 1 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.6014 (ttt) REVERT: L 81 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8753 (mt) REVERT: L 183 MET cc_start: 0.6777 (pmm) cc_final: 0.6046 (ptt) REVERT: L 217 GLU cc_start: 0.7872 (tp30) cc_final: 0.7456 (pt0) REVERT: M 245 MET cc_start: 0.8587 (mmm) cc_final: 0.8309 (ttm) REVERT: N 335 MET cc_start: 0.8751 (ttp) cc_final: 0.8484 (ttp) REVERT: O 1 MET cc_start: 0.6849 (tpp) cc_final: 0.6264 (tpt) REVERT: O 30 THR cc_start: 0.7294 (p) cc_final: 0.6984 (t) REVERT: O 34 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8309 (m) REVERT: O 201 ASP cc_start: 0.7295 (t0) cc_final: 0.6969 (t0) REVERT: O 265 GLU cc_start: 0.7889 (tt0) cc_final: 0.7390 (tt0) REVERT: O 335 MET cc_start: 0.8840 (tmm) cc_final: 0.8455 (tmm) REVERT: P 148 ASP cc_start: 0.6801 (p0) cc_final: 0.6545 (p0) REVERT: P 167 LYS cc_start: 0.6082 (mptt) cc_final: 0.5768 (mtmt) outliers start: 92 outliers final: 62 residues processed: 334 average time/residue: 0.3756 time to fit residues: 202.5281 Evaluate side-chains 323 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 245 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 37 GLN 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 G residue 70 SER Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 245 MET 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 86 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 215 PHE Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 148 ILE 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 M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 34 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 134 SER Chi-restraints excluded: chain O residue 226 ILE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain O residue 324 SER Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 164 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 0.0980 chunk 309 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 300 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 131 optimal weight: 0.0980 chunk 236 optimal weight: 1.9990 chunk 92 optimal weight: 40.0000 chunk 271 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 299 optimal weight: 0.0030 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 HIS ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.8126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28088 Z= 0.171 Angle : 0.604 13.909 38271 Z= 0.303 Chirality : 0.043 0.214 4389 Planarity : 0.004 0.058 4745 Dihedral : 11.924 179.407 4355 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 2.38 % Allowed : 24.60 % Favored : 73.02 % 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: -0.85 (0.15), residues: 3341 helix: 0.49 (0.16), residues: 1199 sheet: 0.07 (0.23), residues: 562 loop : -1.65 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP J 42 HIS 0.004 0.001 HIS L 57 PHE 0.030 0.001 PHE C 288 TYR 0.013 0.001 TYR J 26 ARG 0.014 0.000 ARG F 35 *********************** 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 328 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 261 time to evaluate : 3.403 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: C 26 LEU cc_start: 0.6391 (tp) cc_final: 0.6122 (tt) REVERT: C 63 SER cc_start: 0.5654 (m) cc_final: 0.5054 (p) REVERT: C 94 ASN cc_start: 0.1259 (OUTLIER) cc_final: 0.1022 (t0) REVERT: C 111 MET cc_start: -0.0005 (mmm) cc_final: -0.0689 (ptt) REVERT: C 155 LEU cc_start: 0.0520 (OUTLIER) cc_final: 0.0242 (mt) REVERT: C 191 GLU cc_start: 0.4986 (OUTLIER) cc_final: 0.4534 (pt0) REVERT: C 259 ILE cc_start: 0.3232 (mt) cc_final: 0.2955 (tt) REVERT: C 262 PHE cc_start: 0.6320 (t80) cc_final: 0.5931 (t80) REVERT: D 37 GLN cc_start: 0.6706 (OUTLIER) cc_final: 0.5972 (tp40) REVERT: D 105 TRP cc_start: 0.6139 (m100) cc_final: 0.5421 (m100) REVERT: E 88 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8534 (mmtt) REVERT: G 70 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8231 (p) REVERT: H 29 ASP cc_start: 0.8646 (t0) cc_final: 0.8342 (m-30) REVERT: H 75 GLU cc_start: 0.6736 (tt0) cc_final: 0.6103 (mm-30) REVERT: H 79 GLU cc_start: 0.8039 (pm20) cc_final: 0.7211 (mm-30) REVERT: H 82 GLU cc_start: 0.4130 (pm20) cc_final: 0.3781 (pm20) REVERT: H 88 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8059 (ptmm) REVERT: I 28 GLU cc_start: 0.6898 (tt0) cc_final: 0.6443 (tm-30) REVERT: I 108 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7814 (tt0) REVERT: I 205 VAL cc_start: 0.6630 (t) cc_final: 0.6370 (t) REVERT: I 213 VAL cc_start: 0.6568 (m) cc_final: 0.6221 (p) REVERT: I 230 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6088 (pp20) REVERT: I 276 PRO cc_start: 0.4116 (Cg_endo) cc_final: 0.3678 (Cg_exo) REVERT: I 288 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8012 (mp0) REVERT: I 293 ILE cc_start: 0.5335 (tp) cc_final: 0.4975 (mt) REVERT: I 327 GLU cc_start: 0.7109 (tt0) cc_final: 0.6908 (tt0) REVERT: J 54 MET cc_start: 0.8928 (tpp) cc_final: 0.8382 (tpp) REVERT: J 245 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6242 (mtp) REVERT: J 316 ASP cc_start: 0.8247 (m-30) cc_final: 0.7870 (p0) REVERT: K 155 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.7050 (tpt170) REVERT: K 202 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8558 (pp) REVERT: L 1 MET cc_start: 0.6329 (ttm) cc_final: 0.6104 (ttm) REVERT: L 183 MET cc_start: 0.6786 (pmm) cc_final: 0.6016 (ptt) REVERT: M 293 ILE cc_start: 0.9059 (tp) cc_final: 0.8788 (mt) REVERT: N 335 MET cc_start: 0.8739 (ttp) cc_final: 0.8321 (ttt) REVERT: O 1 MET cc_start: 0.6767 (tpp) cc_final: 0.6307 (tpt) REVERT: O 201 ASP cc_start: 0.7227 (t0) cc_final: 0.6921 (t0) REVERT: O 265 GLU cc_start: 0.7835 (tt0) cc_final: 0.7448 (tt0) REVERT: O 335 MET cc_start: 0.8819 (tmm) cc_final: 0.8493 (tmm) REVERT: P 167 LYS cc_start: 0.6072 (mptt) cc_final: 0.5756 (mtmt) outliers start: 67 outliers final: 48 residues processed: 314 average time/residue: 0.4168 time to fit residues: 214.0830 Evaluate side-chains 299 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 243 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 245 MET 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 77 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 215 PHE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 96 THR 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 M residue 239 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain O residue 324 SER Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.0070 chunk 318 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 333 optimal weight: 6.9990 chunk 307 optimal weight: 20.0000 chunk 265 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 ASN ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.8393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28088 Z= 0.211 Angle : 0.618 13.677 38271 Z= 0.312 Chirality : 0.044 0.290 4389 Planarity : 0.004 0.066 4745 Dihedral : 11.898 179.602 4355 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.06 % Favored : 92.88 % Rotamer: Outliers : 2.27 % Allowed : 25.06 % Favored : 72.67 % 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: -0.81 (0.15), residues: 3341 helix: 0.52 (0.16), residues: 1200 sheet: 0.08 (0.23), residues: 567 loop : -1.63 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP J 42 HIS 0.005 0.001 HIS K 57 PHE 0.034 0.001 PHE C 288 TYR 0.014 0.001 TYR C 157 ARG 0.014 0.000 ARG F 35 ********************** 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 316 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 252 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LEU cc_start: 0.6361 (tp) cc_final: 0.6114 (tt) REVERT: C 155 LEU cc_start: 0.0512 (OUTLIER) cc_final: 0.0244 (mt) REVERT: C 191 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4580 (pt0) REVERT: C 259 ILE cc_start: 0.3163 (mt) cc_final: 0.2889 (tt) REVERT: C 262 PHE cc_start: 0.6469 (t80) cc_final: 0.6065 (t80) REVERT: D 37 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6043 (tp40) REVERT: D 105 TRP cc_start: 0.6369 (m100) cc_final: 0.5609 (m100) REVERT: E 88 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8593 (mmtt) REVERT: G 70 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.8091 (p) REVERT: H 29 ASP cc_start: 0.8656 (t0) cc_final: 0.8342 (m-30) REVERT: H 75 GLU cc_start: 0.6612 (tt0) cc_final: 0.6266 (mm-30) REVERT: H 88 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8114 (ptmm) REVERT: I 28 GLU cc_start: 0.7016 (tt0) cc_final: 0.6520 (tm-30) REVERT: I 205 VAL cc_start: 0.6740 (t) cc_final: 0.6503 (t) REVERT: I 213 VAL cc_start: 0.6419 (m) cc_final: 0.6004 (p) REVERT: I 230 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5842 (pp20) REVERT: I 288 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8019 (mp0) REVERT: I 293 ILE cc_start: 0.5462 (tp) cc_final: 0.5138 (mt) REVERT: J 54 MET cc_start: 0.8971 (tpp) cc_final: 0.8389 (tpp) REVERT: K 104 GLN cc_start: 0.8428 (pm20) cc_final: 0.8105 (mm-40) REVERT: K 155 ARG cc_start: 0.7571 (mtt-85) cc_final: 0.7167 (tpt170) REVERT: K 202 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8597 (pp) REVERT: K 293 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9029 (tp) REVERT: L 1 MET cc_start: 0.6357 (ttm) cc_final: 0.5929 (ttm) REVERT: M 54 MET cc_start: 0.8091 (tpp) cc_final: 0.7233 (tpp) REVERT: M 293 ILE cc_start: 0.9067 (tp) cc_final: 0.8804 (mt) REVERT: N 335 MET cc_start: 0.8783 (ttp) cc_final: 0.8520 (ttp) REVERT: O 1 MET cc_start: 0.6791 (tpp) cc_final: 0.6200 (tpt) REVERT: O 30 THR cc_start: 0.7305 (p) cc_final: 0.6986 (t) REVERT: O 201 ASP cc_start: 0.7279 (t0) cc_final: 0.6930 (t0) REVERT: O 265 GLU cc_start: 0.7828 (tt0) cc_final: 0.7451 (tt0) REVERT: O 335 MET cc_start: 0.8874 (tmm) cc_final: 0.8507 (tmm) REVERT: P 148 ASP cc_start: 0.7196 (p0) cc_final: 0.6853 (p0) REVERT: P 167 LYS cc_start: 0.6160 (mptt) cc_final: 0.5812 (mtmt) outliers start: 64 outliers final: 50 residues processed: 302 average time/residue: 0.3779 time to fit residues: 185.3217 Evaluate side-chains 293 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 236 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 86 THR 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 77 THR 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 263 VAL Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain K residue 306 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 96 THR 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 M residue 239 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 250 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 322 VAL Chi-restraints excluded: chain P residue 87 ASN Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 266 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 0.0030 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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 = 0.4134 r_free = 0.4134 target = 0.137962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.099983 restraints weight = 61575.750| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.11 r_work: 0.3345 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.8415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 28088 Z= 0.293 Angle : 0.752 59.199 38271 Z= 0.404 Chirality : 0.044 0.308 4389 Planarity : 0.004 0.078 4745 Dihedral : 11.905 179.603 4355 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.21 % Favored : 92.73 % Rotamer: Outliers : 2.27 % Allowed : 24.99 % Favored : 72.74 % Cbeta Deviations : 0.03 % 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: -0.83 (0.15), residues: 3341 helix: 0.52 (0.16), residues: 1200 sheet: 0.01 (0.23), residues: 569 loop : -1.64 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 180 HIS 0.005 0.001 HIS K 57 PHE 0.050 0.001 PHE H 20 TYR 0.014 0.001 TYR C 157 ARG 0.030 0.000 ARG I 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6112.93 seconds wall clock time: 112 minutes 34.03 seconds (6754.03 seconds total)