Starting phenix.real_space_refine on Mon Aug 5 07:41:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihm_35449/08_2024/8ihm_35449.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihm_35449/08_2024/8ihm_35449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihm_35449/08_2024/8ihm_35449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihm_35449/08_2024/8ihm_35449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihm_35449/08_2024/8ihm_35449.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihm_35449/08_2024/8ihm_35449.cif" } resolution = 3.58 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= 0.002 sd= 0.051 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 317 5.49 5 S 12 5.16 5 C 7266 2.51 5 N 2473 2.21 5 O 3085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 134": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "M GLU 60": "OE1" <-> "OE2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 114": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13153 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 607 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 801 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 779 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ML3:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 609 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 760 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 639 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3216 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3280 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 154 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "N" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 841 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 7.75, per 1000 atoms: 0.59 Number of scatterers: 13153 At special positions: 0 Unit cell: (93.09, 140.17, 116.63, 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 12 16.00 P 317 15.00 O 3085 8.00 N 2473 7.00 C 7266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 20 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 23 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 20 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 23 Secondary structure from input PDB file: 39 helices and 9 sheets defined 65.6% alpha, 4.2% beta 150 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 6.05 Creating SS restraints... Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.569A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 115 removed outlier: 3.861A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.650A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.228A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.776A pdb=" N TYR B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.771A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.651A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.560A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.561A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.553A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 74 removed outlier: 3.963A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 71 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 81 Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.830A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.769A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.710A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.581A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.673A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.656A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.621A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.692A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.738A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 54 through 81 removed outlier: 3.778A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.533A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.568A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 74 removed outlier: 4.358A pdb=" N GLY N 74 " --> pdb=" O GLU N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 131 removed outlier: 3.570A pdb=" N LYS N 108 " --> pdb=" O ASN N 104 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS N 120 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN N 125 " --> pdb=" O SER N 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.052A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.051A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.177A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.440A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.589A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'N' and resid 79 through 81 removed outlier: 3.588A pdb=" N LEU N 21 " --> pdb=" O HIS N 18 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA N 16 " --> pdb=" O TYR N 23 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS N 14 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 15 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.445A pdb=" N ASP N 32 " --> pdb=" O MET N 37 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET N 37 " --> pdb=" O ASP N 32 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 388 hydrogen bonds 776 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 4.75 Time building geometry restraints manager: 7.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2231 1.33 - 1.45: 4788 1.45 - 1.57: 6363 1.57 - 1.69: 632 1.69 - 1.81: 22 Bond restraints: 14036 Sorted by residual: bond pdb=" CA SER B 47 " pdb=" C SER B 47 " ideal model delta sigma weight residual 1.524 1.476 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" SG ML3 E 36 " pdb=" CD ML3 E 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.55e+00 bond pdb=" CA ALA D 74 " pdb=" C ALA D 74 " ideal model delta sigma weight residual 1.524 1.458 0.066 2.25e-02 1.98e+03 8.52e+00 bond pdb=" CA TYR A 99 " pdb=" C TYR A 99 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.35e-02 5.49e+03 7.10e+00 bond pdb=" CB ML3 E 36 " pdb=" SG ML3 E 36 " ideal model delta sigma weight residual 1.817 1.765 0.052 2.00e-02 2.50e+03 6.66e+00 ... (remaining 14031 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.24: 1430 105.24 - 112.45: 7898 112.45 - 119.65: 4466 119.65 - 126.86: 5683 126.86 - 134.07: 855 Bond angle restraints: 20332 Sorted by residual: angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 111.81 102.06 9.75 8.60e-01 1.35e+00 1.29e+02 angle pdb=" N ARG N 98 " pdb=" CA ARG N 98 " pdb=" C ARG N 98 " ideal model delta sigma weight residual 109.72 98.23 11.49 1.60e+00 3.91e-01 5.15e+01 angle pdb=" N GLU A 97 " pdb=" CA GLU A 97 " pdb=" C GLU A 97 " ideal model delta sigma weight residual 111.40 103.25 8.15 1.22e+00 6.72e-01 4.46e+01 angle pdb=" N LEU E 48 " pdb=" CA LEU E 48 " pdb=" C LEU E 48 " ideal model delta sigma weight residual 111.14 104.49 6.65 1.08e+00 8.57e-01 3.80e+01 angle pdb=" N ILE N 72 " pdb=" CA ILE N 72 " pdb=" C ILE N 72 " ideal model delta sigma weight residual 112.50 119.83 -7.33 1.39e+00 5.18e-01 2.78e+01 ... (remaining 20327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 6045 35.51 - 71.01: 1493 71.01 - 106.52: 42 106.52 - 142.02: 4 142.02 - 177.53: 3 Dihedral angle restraints: 7587 sinusoidal: 5027 harmonic: 2560 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C4' DC I -73 " pdb=" C3' DC I -73 " pdb=" O3' DC I -73 " pdb=" P DT I -72 " ideal model delta sinusoidal sigma weight residual -140.00 37.53 -177.53 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 56.50 163.50 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1368 0.032 - 0.064: 678 0.064 - 0.096: 185 0.096 - 0.128: 61 0.128 - 0.160: 9 Chirality restraints: 2301 Sorted by residual: chirality pdb=" CA ARG N 98 " pdb=" N ARG N 98 " pdb=" C ARG N 98 " pdb=" CB ARG N 98 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA PRO G 80 " pdb=" N PRO G 80 " pdb=" C PRO G 80 " pdb=" CB PRO G 80 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ALA D 74 " pdb=" N ALA D 74 " pdb=" C ALA D 74 " pdb=" CB ALA D 74 " both_signs ideal model delta sigma weight residual False 2.48 2.34 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2298 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 63 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C GLU F 63 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU F 63 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN F 64 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 66 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 8 " -0.027 2.00e-02 2.50e+03 1.23e-02 4.57e+00 pdb=" N9 DG J 8 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG J 8 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DG J 8 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J 8 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG J 8 " -0.010 2.00e-02 2.50e+03 pdb=" O6 DG J 8 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DG J 8 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG J 8 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG J 8 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG J 8 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 8 " 0.001 2.00e-02 2.50e+03 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3530 2.82 - 3.34: 13386 3.34 - 3.86: 25816 3.86 - 4.38: 29084 4.38 - 4.90: 39690 Nonbonded interactions: 111506 Sorted by model distance: nonbonded pdb=" O ILE M 54 " pdb=" OG1 THR M 55 " model vdw 2.297 3.040 nonbonded pdb=" C3' DT I 71 " pdb=" C1' DT I 71 " model vdw 2.319 3.120 nonbonded pdb=" OP1 DT I 12 " pdb=" N GLY N 83 " model vdw 2.365 3.120 nonbonded pdb=" N3 DC I -73 " pdb=" N2 DG J 74 " model vdw 2.372 3.200 nonbonded pdb=" O SER M 62 " pdb=" OG SER M 62 " model vdw 2.399 3.040 ... (remaining 111501 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 'A' and (resid 38 through 45 or (resid 46 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 through 62 or (r \ esid 63 and (name N or name CA or name C or name O or name CB )) or resid 64 thr \ ough 70 or (resid 71 through 72 and (name N or name CA or name C or name O or na \ me CB )) or resid 73 through 81 or (resid 82 and (name N or name CA or name C or \ name O or name CB )) or resid 83 through 89 or (resid 90 through 91 and (name N \ or name CA or name C or name O or name CB )) or resid 92 through 96 or (resid 9 \ 7 through 98 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 9 or (resid 100 through 102 and (name N or name CA or name C or name O or name C \ B )) or resid 103 or (resid 104 through 108 and (name N or name CA or name C or \ name O or name CB )) or resid 109 through 134)) selection = (chain 'E' and (resid 38 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 74 or (r \ esid 75 and (name N or name CA or name C or name O )) or resid 76 through 87 or \ (resid 88 and (name N or name CA or name C or name O )) or resid 89 through 104 \ or (resid 105 through 108 and (name N or name CA or name C or name O or name CB \ )) or resid 109 through 114 or (resid 115 through 116 and (name N or name CA or \ name C or name O or name CB )) or resid 117 or (resid 118 and (name N or name CA \ or name C or name O or name CB )) or resid 119 or (resid 120 and (name N or nam \ e CA or name C or name O or name CB )) or resid 121 through 134)) } ncs_group { reference = (chain 'B' and (resid 22 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 29 or (resid 30 through 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 35 or (res \ id 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 50 or (resid 51 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 52 th \ rough 61 or (resid 62 and (name N or name CA or name C or name O or name CB )) o \ r resid 63 through 64 or (resid 65 through 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 through 77 or (resid 78 through 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 or (resid 82 through \ 83 and (name N or name CA or name C or name O or name CB )) or resid 84 or (resi \ d 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 101)) selection = (chain 'F' and (resid 22 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 34 or (resid 35 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1)) or resid 36 through 44 or (resid 45 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 70 or (resid 71 and (n \ ame N or name CA or name C or name O or name CB )) or resid 72 or (resid 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 90 or ( \ resid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 th \ rough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) o \ r resid 98 through 99 or (resid 100 and (name N or name CA or name C or name O o \ r name CB )) or resid 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 15 or (resid 16 and (name N or name CA or name \ C or name O )) or resid 17 through 24 or (resid 25 and (name N or name CA or nam \ e C or name O or name CB )) or resid 26 through 35 or (resid 36 and (name N or n \ ame CA or name C or name O or name CB )) or resid 37 through 40 or (resid 41 and \ (name N or name CA or name C or name O or name CB )) or resid 42 through 55 or \ (resid 56 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1)) or resid 57 or (resid 58 through 60 and (name N or name CA o \ r name C or name O or name CB )) or resid 61 through 62 or (resid 63 and (name N \ or name CA or name C or name O or name CB )) or resid 64 through 76 or (resid 7 \ 7 through 78 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 9 through 80 or (resid 81 and (name N or name CA or name C or name O or name CB \ )) or resid 82 through 84 or (resid 85 through 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 89 or (resid 90 and (name N or na \ me CA or name C or name O or name CB )) or resid 91 through 94 or (resid 95 and \ (name N or name CA or name C or name O or name CB )) or resid 96 through 114 or \ (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 116 \ through 117)) selection = (chain 'G' and (resid 12 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 48 or (resid 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 58 or (res \ id 59 through 60 and (name N or name CA or name C or name O or name CB )) or res \ id 61 through 77 or (resid 78 and (name N or name CA or name C or name O or name \ CB )) or resid 79 through 86 or (resid 87 and (name N or name CA or name C or n \ ame O or name CB )) or resid 88 through 100 or (resid 101 and (name N or name CA \ or name C or name O or name CB )) or resid 102 through 117)) } ncs_group { reference = (chain 'D' and ((resid 33 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 or (resid 57 through 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 84 or (re \ sid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 or ( \ resid 87 through 90 and (name N or name CA or name C or name O or name CB )) or \ resid 91 through 121)) selection = (chain 'H' and (resid 33 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 59 or (resid 60 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 83 or (resid 84 through 85 and (name N or name CA or name C or name O or name \ CB )) or resid 86 through 87 or (resid 88 through 90 and (name N or name CA or \ name C or name O or name CB )) or resid 91 through 111 or (resid 112 and (name N \ or name CA or name C or name O or name CB )) or resid 113 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.070 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 14036 Z= 0.425 Angle : 0.752 11.488 20332 Z= 0.469 Chirality : 0.041 0.160 2301 Planarity : 0.004 0.054 1495 Dihedral : 29.269 177.526 5929 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: -3.94 (0.23), residues: 861 helix: -2.84 (0.17), residues: 548 sheet: -2.63 (1.01), residues: 19 loop : -1.68 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 91 HIS 0.003 0.001 HIS N 18 PHE 0.023 0.002 PHE C 25 TYR 0.014 0.002 TYR D 37 ARG 0.006 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.050 Fit side-chains REVERT: B 77 LYS cc_start: 0.8833 (mttm) cc_final: 0.8613 (mmtt) REVERT: C 38 ASN cc_start: 0.8345 (m110) cc_final: 0.7689 (m110) REVERT: E 94 GLU cc_start: 0.8384 (tp30) cc_final: 0.8150 (tp30) REVERT: F 84 MET cc_start: 0.8148 (tpp) cc_final: 0.7889 (tpp) REVERT: H 106 HIS cc_start: 0.8097 (m-70) cc_final: 0.7801 (m-70) REVERT: N 114 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8389 (tm-30) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3152 time to fit residues: 78.4894 Evaluate side-chains 153 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 79 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14036 Z= 0.279 Angle : 0.659 7.158 20332 Z= 0.384 Chirality : 0.038 0.136 2301 Planarity : 0.005 0.051 1495 Dihedral : 32.084 174.540 4413 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.77 % Allowed : 13.64 % Favored : 84.59 % 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: -1.33 (0.27), residues: 861 helix: -0.54 (0.21), residues: 581 sheet: -1.97 (1.01), residues: 19 loop : -1.26 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 31 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.002 PHE C 25 TYR 0.015 0.002 TYR F 88 ARG 0.004 0.000 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 0.878 Fit side-chains REVERT: B 53 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8177 (tm-30) REVERT: B 77 LYS cc_start: 0.8932 (mttm) cc_final: 0.8520 (mmtt) REVERT: D 120 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8579 (m) REVERT: E 81 ASP cc_start: 0.7917 (t0) cc_final: 0.7665 (t0) REVERT: H 106 HIS cc_start: 0.8018 (m-70) cc_final: 0.7569 (m-70) REVERT: N 37 MET cc_start: 0.7768 (ppp) cc_final: 0.7416 (ppp) REVERT: N 65 GLU cc_start: 0.4913 (tt0) cc_final: 0.4450 (tt0) REVERT: N 110 ARG cc_start: 0.7875 (mmp80) cc_final: 0.7446 (mmp80) REVERT: N 114 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8110 (tm-30) outliers start: 11 outliers final: 7 residues processed: 161 average time/residue: 0.2722 time to fit residues: 63.0682 Evaluate side-chains 152 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 54 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14036 Z= 0.231 Angle : 0.618 9.490 20332 Z= 0.360 Chirality : 0.036 0.169 2301 Planarity : 0.004 0.040 1495 Dihedral : 31.891 173.623 4413 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.73 % Allowed : 15.89 % Favored : 81.38 % 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: -0.04 (0.28), residues: 861 helix: 0.54 (0.22), residues: 574 sheet: -1.22 (1.15), residues: 19 loop : -1.00 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 31 HIS 0.006 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.013 0.001 TYR B 98 ARG 0.003 0.000 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.019 Fit side-chains REVERT: B 53 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8081 (tm-30) REVERT: B 77 LYS cc_start: 0.8895 (mttm) cc_final: 0.8500 (mmtt) REVERT: B 98 TYR cc_start: 0.8710 (m-10) cc_final: 0.8460 (m-80) REVERT: E 81 ASP cc_start: 0.7774 (t0) cc_final: 0.7560 (t0) REVERT: G 35 ARG cc_start: 0.9115 (mtm-85) cc_final: 0.8257 (mtm-85) REVERT: G 97 LEU cc_start: 0.8243 (mp) cc_final: 0.7870 (mt) REVERT: H 106 HIS cc_start: 0.7468 (m90) cc_final: 0.7118 (m-70) REVERT: N 107 MET cc_start: 0.6238 (tmm) cc_final: 0.6020 (tmm) REVERT: N 110 ARG cc_start: 0.7944 (mmp80) cc_final: 0.7646 (mmp80) outliers start: 17 outliers final: 9 residues processed: 161 average time/residue: 0.2739 time to fit residues: 63.0574 Evaluate side-chains 148 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14036 Z= 0.313 Angle : 0.648 6.949 20332 Z= 0.374 Chirality : 0.038 0.151 2301 Planarity : 0.004 0.044 1495 Dihedral : 31.932 175.273 4413 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.05 % Allowed : 17.66 % Favored : 79.29 % 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: 0.21 (0.29), residues: 861 helix: 0.77 (0.22), residues: 573 sheet: -1.48 (1.08), residues: 19 loop : -0.95 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 91 HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE N 78 TYR 0.012 0.001 TYR B 98 ARG 0.004 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8050 (m-30) cc_final: 0.7848 (p0) REVERT: B 53 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8179 (tm-30) REVERT: B 77 LYS cc_start: 0.8908 (mttm) cc_final: 0.8488 (mmtt) REVERT: B 98 TYR cc_start: 0.8796 (m-10) cc_final: 0.8540 (m-10) REVERT: E 81 ASP cc_start: 0.7933 (t0) cc_final: 0.7674 (t0) REVERT: G 23 LEU cc_start: 0.7569 (mt) cc_final: 0.7367 (mp) REVERT: G 35 ARG cc_start: 0.9135 (mtm-85) cc_final: 0.8241 (mtm-85) REVERT: H 81 ASN cc_start: 0.8104 (m-40) cc_final: 0.7858 (m-40) REVERT: H 106 HIS cc_start: 0.7673 (m90) cc_final: 0.7256 (m-70) REVERT: N 65 GLU cc_start: 0.5020 (OUTLIER) cc_final: 0.4315 (tt0) outliers start: 19 outliers final: 15 residues processed: 153 average time/residue: 0.3114 time to fit residues: 67.1864 Evaluate side-chains 151 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.0374 > 50: distance: 68 - 90: 17.940 distance: 78 - 82: 11.975 distance: 79 - 107: 10.494 distance: 82 - 83: 16.860 distance: 83 - 84: 12.767 distance: 83 - 86: 6.713 distance: 84 - 85: 7.890 distance: 84 - 90: 4.552 distance: 85 - 112: 8.192 distance: 86 - 87: 20.378 distance: 86 - 88: 22.609 distance: 87 - 89: 24.920 distance: 90 - 91: 3.626 distance: 91 - 92: 12.323 distance: 91 - 94: 14.331 distance: 92 - 93: 8.485 distance: 92 - 99: 9.033 distance: 94 - 95: 16.133 distance: 95 - 96: 3.952 distance: 96 - 97: 6.595 distance: 96 - 98: 8.586 distance: 99 - 100: 9.986 distance: 100 - 101: 14.605 distance: 100 - 103: 13.942 distance: 101 - 102: 20.554 distance: 101 - 107: 14.980 distance: 102 - 134: 15.774 distance: 103 - 104: 20.615 distance: 104 - 105: 28.819 distance: 104 - 106: 7.043 distance: 107 - 108: 9.156 distance: 108 - 109: 11.783 distance: 108 - 111: 17.053 distance: 109 - 110: 9.661 distance: 109 - 112: 8.216 distance: 112 - 113: 6.156 distance: 113 - 114: 34.729 distance: 113 - 116: 14.250 distance: 114 - 115: 13.353 distance: 114 - 123: 27.750 distance: 116 - 117: 30.375 distance: 117 - 118: 27.033 distance: 118 - 119: 13.406 distance: 119 - 120: 6.755 distance: 120 - 121: 24.611 distance: 120 - 122: 11.369 distance: 123 - 124: 6.132 distance: 124 - 125: 9.955 distance: 124 - 127: 23.542 distance: 125 - 126: 27.890 distance: 125 - 134: 19.540 distance: 127 - 128: 18.742 distance: 128 - 129: 33.771 distance: 129 - 130: 4.788 distance: 130 - 131: 16.363 distance: 131 - 132: 12.024 distance: 131 - 133: 19.406 distance: 134 - 135: 12.533 distance: 135 - 136: 15.161 distance: 135 - 138: 15.043 distance: 136 - 137: 42.487 distance: 136 - 142: 21.844 distance: 138 - 139: 18.493 distance: 138 - 140: 14.144 distance: 139 - 141: 32.083 distance: 142 - 143: 14.430 distance: 143 - 144: 16.032 distance: 143 - 146: 10.276 distance: 144 - 145: 11.953 distance: 144 - 153: 13.964 distance: 146 - 147: 10.958 distance: 147 - 148: 10.053 distance: 148 - 149: 9.875 distance: 149 - 150: 10.310 distance: 150 - 151: 6.241 distance: 150 - 152: 17.719 distance: 153 - 154: 18.531 distance: 154 - 155: 16.358 distance: 155 - 156: 17.505 distance: 155 - 157: 11.268 distance: 157 - 158: 3.728 distance: 158 - 159: 8.609 distance: 158 - 161: 8.971 distance: 159 - 160: 17.229 distance: 159 - 166: 3.829 distance: 161 - 162: 11.318 distance: 162 - 163: 6.551 distance: 163 - 164: 6.080 distance: 163 - 165: 9.738