Starting phenix.real_space_refine on Fri Aug 9 23:20:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/08_2024/7tr6_26081_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/08_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_26081/08_2024/7tr6_26081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/08_2024/7tr6_26081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/08_2024/7tr6_26081_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tr6_26081/08_2024/7tr6_26081_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 59 5.16 5 C 17422 2.51 5 N 4681 2.21 5 O 5243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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-5409/modules/chem_data/mon_lib" Total number of atoms: 27449 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "E" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "I" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2494 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2134 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "R" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 949 Classifications: {'RNA': 45} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 13, 'rna3p_pyr': 13} Link IDs: {'rna2p': 18, 'rna3p': 26} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 16.50, per 1000 atoms: 0.60 Number of scatterers: 27449 At special positions: 0 Unit cell: (112.205, 129.086, 204.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 44 15.00 O 5243 8.00 N 4681 7.00 C 17422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 12.34 Conformation dependent library (CDL) restraints added in 5.1 seconds 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6270 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 41 sheets defined 38.3% alpha, 11.9% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 9.68 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: 8.16 Time building geometry restraints manager: 13.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8108 1.33 - 1.45: 4387 1.45 - 1.57: 15399 1.57 - 1.69: 88 1.69 - 1.81: 106 Bond restraints: 28088 Sorted by residual: bond pdb=" CA VAL I 279 " pdb=" CB VAL I 279 " ideal model delta sigma weight residual 1.553 1.540 0.013 7.40e-03 1.83e+04 3.08e+00 bond pdb=" N TYR C 211 " pdb=" CA TYR C 211 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.33e+00 bond pdb=" CA LEU C 207 " pdb=" CB LEU C 207 " ideal model delta sigma weight residual 1.522 1.532 -0.010 7.00e-03 2.04e+04 2.06e+00 bond pdb=" C3' A R 1 " pdb=" O3' A R 1 " ideal model delta sigma weight residual 1.415 1.438 -0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" CB GLU I 284 " pdb=" CG GLU I 284 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 28083 not shown) Histogram of bond angle deviations from ideal: 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 3.040 nonbonded pdb=" NH1 ARG P 110 " pdb=" OE1 GLU P 112 " model vdw 2.148 3.120 nonbonded pdb=" OD1 ASP K 65 " pdb=" OH TYR K 83 " model vdw 2.164 3.040 nonbonded pdb=" O ASN J 253 " pdb=" OG SER J 257 " model vdw 2.167 3.040 nonbonded pdb=" O2' A R 1 " pdb=" OP2 U R 2 " model vdw 2.188 3.040 ... (remaining 227237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and resid 3 through 109) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 164 or resid 180 th \ rough 335)) selection = (chain 'J' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 164 or resid 180 through 335)) selection = (chain 'K' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'L' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'M' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'N' and resid 1 through 335) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.440 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: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.280 Process input model: 81.770 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.720 ------------------------------------------------------------------------------- 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 : 2.748 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: 0.3774 time to fit residues: 424.1871 Evaluate side-chains 363 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 304 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: