Starting phenix.real_space_refine on Mon Mar 18 21:26:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/03_2024/6k0a_30036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/03_2024/6k0a_30036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/03_2024/6k0a_30036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/03_2024/6k0a_30036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/03_2024/6k0a_30036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/03_2024/6k0a_30036.pdb" } resolution = 4.6 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= 0.001 sd= 0.005 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 516 5.49 5 S 38 5.16 5 C 12184 2.51 5 N 4012 2.21 5 O 5524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 101": "OD1" <-> "OD2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "E ASP 48": "OD1" <-> "OD2" Residue "E ASP 57": "OD1" <-> "OD2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 105": "NH1" <-> "NH2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "I TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I ASP 80": "OD1" <-> "OD2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "F ASP 48": "OD1" <-> "OD2" Residue "F ASP 57": "OD1" <-> "OD2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "J TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 67": "OE1" <-> "OE2" Residue "J ASP 80": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22276 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "C" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1875 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "E" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "G" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1021 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "X" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5535 Classifications: {'RNA': 258} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 131, 'rna3p_pyr': 99} Link IDs: {'rna2p': 28, 'rna3p': 229} Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "D" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1875 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "F" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1021 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "Y" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5535 Classifications: {'RNA': 258} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 131, 'rna3p_pyr': 99} Link IDs: {'rna2p': 28, 'rna3p': 229} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4232 SG CYS G 63 182.893 49.953 84.315 1.00123.20 S ATOM 4256 SG CYS G 66 180.141 52.933 85.267 1.00109.97 S ATOM 4470 SG CYS G 92 183.213 53.629 87.634 1.00128.27 S ATOM 4493 SG CYS G 95 181.038 50.386 87.761 1.00145.27 S ATOM 15369 SG CYS H 63 61.161 109.147 84.323 1.00124.80 S ATOM 15393 SG CYS H 66 63.897 106.167 85.323 1.00107.16 S ATOM 15607 SG CYS H 92 60.790 105.479 87.646 1.00135.20 S ATOM 15630 SG CYS H 95 62.965 108.721 87.797 1.00143.38 S Time building chain proxies: 11.60, per 1000 atoms: 0.52 Number of scatterers: 22276 At special positions: 0 Unit cell: (245.25, 161.32, 109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 38 16.00 P 516 15.00 O 5524 8.00 N 4012 7.00 C 12184 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: 9.48 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 66 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 63 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 95 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 92 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 63 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 95 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 92 " Number of angles added : 12 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 46.3% alpha, 15.0% beta 120 base pairs and 324 stacking pairs defined. Time for finding SS restraints: 8.46 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.597A pdb=" N ASN A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.554A pdb=" N GLY A 50 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 53 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.675A pdb=" N VAL A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.960A pdb=" N ILE A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 removed outlier: 4.061A pdb=" N VAL A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 124 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 21 removed outlier: 3.542A pdb=" N LYS C 18 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 47 removed outlier: 3.583A pdb=" N GLU C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 43 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 75 removed outlier: 3.642A pdb=" N ASP C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.993A pdb=" N VAL C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.515A pdb=" N ALA C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 121 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.515A pdb=" N ASN C 139 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS C 140 " --> pdb=" O LEU C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 140' Processing helix chain 'C' and resid 141 through 162 removed outlier: 3.548A pdb=" N THR C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 192 removed outlier: 3.667A pdb=" N LEU C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 217 removed outlier: 3.540A pdb=" N LYS C 198 " --> pdb=" O PRO C 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 200 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 202 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N CYS C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 removed outlier: 4.250A pdb=" N LYS E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 82 through 87' Processing helix chain 'G' and resid 4 through 29 removed outlier: 3.777A pdb=" N GLU G 15 " --> pdb=" O LYS G 11 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP G 18 " --> pdb=" O TYR G 14 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET G 21 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU G 26 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 51 removed outlier: 3.543A pdb=" N VAL G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET G 50 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.754A pdb=" N GLU G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 25 removed outlier: 3.684A pdb=" N LYS I 15 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 41 removed outlier: 3.522A pdb=" N VAL I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR I 35 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU I 39 " --> pdb=" O THR I 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 58 removed outlier: 3.909A pdb=" N VAL I 57 " --> pdb=" O PRO I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 removed outlier: 4.409A pdb=" N TYR I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU I 67 " --> pdb=" O TYR I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 86 Processing helix chain 'I' and resid 99 through 101 No H-bonds generated for 'chain 'I' and resid 99 through 101' Processing helix chain 'I' and resid 102 through 110 removed outlier: 3.918A pdb=" N VAL I 107 " --> pdb=" O GLU I 103 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 117 removed outlier: 3.612A pdb=" N LEU I 115 " --> pdb=" O LYS I 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.598A pdb=" N ASN B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.553A pdb=" N GLY B 50 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 53 " --> pdb=" O TRP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.676A pdb=" N VAL B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.958A pdb=" N ILE B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.062A pdb=" N VAL B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 124 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 21 removed outlier: 3.541A pdb=" N LYS D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 removed outlier: 3.584A pdb=" N GLU D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 removed outlier: 3.642A pdb=" N ASP D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS D 70 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS D 73 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 97 removed outlier: 3.993A pdb=" N VAL D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.515A pdb=" N ALA D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 121 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.514A pdb=" N ASN D 139 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS D 140 " --> pdb=" O LEU D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 136 through 140' Processing helix chain 'D' and resid 141 through 162 removed outlier: 3.547A pdb=" N THR D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.666A pdb=" N LEU D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 217 removed outlier: 3.540A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 200 " --> pdb=" O TYR D 196 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 202 " --> pdb=" O LYS D 198 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 removed outlier: 4.248A pdb=" N LYS F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 82 through 87' Processing helix chain 'H' and resid 4 through 29 removed outlier: 3.777A pdb=" N GLU H 15 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP H 18 " --> pdb=" O TYR H 14 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET H 21 " --> pdb=" O ILE H 17 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU H 26 " --> pdb=" O SER H 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU H 27 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 51 removed outlier: 3.545A pdb=" N VAL H 40 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET H 50 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 121 removed outlier: 3.753A pdb=" N GLU H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 25 removed outlier: 3.683A pdb=" N LYS J 15 " --> pdb=" O GLU J 11 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU J 16 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA J 22 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 41 removed outlier: 3.522A pdb=" N VAL J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR J 35 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU J 39 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG J 40 " --> pdb=" O LYS J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 58 removed outlier: 3.907A pdb=" N VAL J 57 " --> pdb=" O PRO J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 removed outlier: 4.409A pdb=" N TYR J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU J 67 " --> pdb=" O TYR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 86 Processing helix chain 'J' and resid 99 through 101 No H-bonds generated for 'chain 'J' and resid 99 through 101' Processing helix chain 'J' and resid 102 through 110 removed outlier: 3.919A pdb=" N VAL J 107 " --> pdb=" O GLU J 103 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 117 removed outlier: 3.613A pdb=" N LEU J 115 " --> pdb=" O LYS J 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.542A pdb=" N VAL A 59 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE A 67 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR A 18 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 100 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 20 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.442A pdb=" N ASP C 4 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR C 28 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN C 6 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE C 25 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY C 56 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE C 27 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LYS C 58 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 80 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 82 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 59 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU C 84 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE C 81 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N SER C 104 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 83 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU C 103 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN C 133 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 223 through 225 removed outlier: 3.767A pdb=" N VAL C 224 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 71 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL E 60 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS E 16 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL E 43 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU E 37 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 44 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 79 through 81 removed outlier: 3.697A pdb=" N ARG G 79 " --> pdb=" O VAL G 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 27 through 29 removed outlier: 4.483A pdb=" N LEU I 45 " --> pdb=" O ILE I 96 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL I 46 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL I 75 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE I 48 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 60 removed outlier: 3.543A pdb=" N VAL B 59 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE B 67 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR B 18 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 100 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 20 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 removed outlier: 6.443A pdb=" N ASP D 4 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR D 28 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN D 6 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE D 25 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY D 56 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE D 27 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS D 58 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE D 80 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 82 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE D 59 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU D 84 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE D 81 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N SER D 104 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 83 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU D 103 " --> pdb=" O GLU D 131 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN D 133 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 223 through 225 removed outlier: 3.775A pdb=" N VAL D 224 " --> pdb=" O LYS F 71 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS F 71 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL F 60 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL F 20 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS F 16 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL F 43 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU F 37 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F 44 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 79 through 81 removed outlier: 3.697A pdb=" N ARG H 79 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 27 through 29 removed outlier: 4.484A pdb=" N LEU J 45 " --> pdb=" O ILE J 96 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL J 46 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL J 75 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE J 48 " --> pdb=" O VAL J 75 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 302 hydrogen bonds 564 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 324 stacking parallelities Total time for adding SS restraints: 6.96 Time building geometry restraints manager: 10.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4782 1.34 - 1.45: 7556 1.45 - 1.57: 10348 1.57 - 1.69: 1030 1.69 - 1.81: 56 Bond restraints: 23772 Sorted by residual: bond pdb=" CA THR C 61 " pdb=" CB THR C 61 " ideal model delta sigma weight residual 1.527 1.557 -0.029 1.61e-02 3.86e+03 3.36e+00 bond pdb=" CA THR D 61 " pdb=" CB THR D 61 " ideal model delta sigma weight residual 1.527 1.556 -0.029 1.61e-02 3.86e+03 3.26e+00 bond pdb=" C3' U Y 198 " pdb=" O3' U Y 198 " ideal model delta sigma weight residual 1.427 1.452 -0.025 1.50e-02 4.44e+03 2.69e+00 bond pdb=" C3' U X 198 " pdb=" O3' U X 198 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.59e+00 bond pdb=" C THR C 105 " pdb=" N PRO C 106 " ideal model delta sigma weight residual 1.333 1.344 -0.011 7.80e-03 1.64e+04 2.01e+00 ... (remaining 23767 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.02: 3237 107.02 - 113.76: 14218 113.76 - 120.49: 9037 120.49 - 127.23: 6925 127.23 - 133.97: 1153 Bond angle restraints: 34570 Sorted by residual: angle pdb=" C LYS C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 122.82 130.31 -7.49 1.42e+00 4.96e-01 2.78e+01 angle pdb=" C LYS D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 122.82 130.31 -7.49 1.42e+00 4.96e-01 2.78e+01 angle pdb=" C3' U X 198 " pdb=" O3' U X 198 " pdb=" P U X 199 " ideal model delta sigma weight residual 120.20 126.54 -6.34 1.50e+00 4.44e-01 1.78e+01 angle pdb=" C3' U Y 198 " pdb=" O3' U Y 198 " pdb=" P U Y 199 " ideal model delta sigma weight residual 120.20 126.50 -6.30 1.50e+00 4.44e-01 1.77e+01 angle pdb=" CA LYS D 50 " pdb=" C LYS D 50 " pdb=" N LEU D 51 " ideal model delta sigma weight residual 115.81 120.48 -4.67 1.15e+00 7.56e-01 1.65e+01 ... (remaining 34565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 13624 35.76 - 71.51: 1428 71.51 - 107.27: 174 107.27 - 143.03: 0 143.03 - 178.79: 6 Dihedral angle restraints: 15232 sinusoidal: 11214 harmonic: 4018 Sorted by residual: dihedral pdb=" O4' U X 207 " pdb=" C1' U X 207 " pdb=" N1 U X 207 " pdb=" C2 U X 207 " ideal model delta sinusoidal sigma weight residual 232.00 53.21 178.79 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U Y 207 " pdb=" C1' U Y 207 " pdb=" N1 U Y 207 " pdb=" C2 U Y 207 " ideal model delta sinusoidal sigma weight residual 232.00 53.24 178.76 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U X 228 " pdb=" C1' U X 228 " pdb=" N1 U X 228 " pdb=" C2 U X 228 " ideal model delta sinusoidal sigma weight residual -160.00 -98.94 -61.06 1 1.50e+01 4.44e-03 2.20e+01 ... (remaining 15229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3910 0.060 - 0.119: 302 0.119 - 0.178: 63 0.178 - 0.238: 7 0.238 - 0.297: 6 Chirality restraints: 4288 Sorted by residual: chirality pdb=" CB ILE H 80 " pdb=" CA ILE H 80 " pdb=" CG1 ILE H 80 " pdb=" CG2 ILE H 80 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE G 80 " pdb=" CA ILE G 80 " pdb=" CG1 ILE G 80 " pdb=" CG2 ILE G 80 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" P U Y 199 " pdb=" OP1 U Y 199 " pdb=" OP2 U Y 199 " pdb=" O5' U Y 199 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4285 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 63 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 64 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 63 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO B 64 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO D 181 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.034 5.00e-02 4.00e+02 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 6327 2.83 - 3.35: 16876 3.35 - 3.87: 40547 3.87 - 4.38: 47212 4.38 - 4.90: 66607 Nonbonded interactions: 177569 Sorted by model distance: nonbonded pdb=" OP1 U X 16 " pdb=" OH TYR D 182 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR J 4 " pdb=" O ALA J 49 " model vdw 2.328 2.440 nonbonded pdb=" OH TYR I 4 " pdb=" O ALA I 49 " model vdw 2.329 2.440 nonbonded pdb=" OP2 G Y 76 " pdb=" O2' A Y 252 " model vdw 2.359 2.440 nonbonded pdb=" OP2 G X 76 " pdb=" O2' A X 252 " model vdw 2.360 2.440 ... (remaining 177564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints Number of NCS constrained groups: 6 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'X' selection = chain 'Y' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 1.270 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: 6.550 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 63.970 Find NCS groups from input model: 0.930 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 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 0.037 23772 Z= 0.177 Angle : 0.703 11.557 34570 Z= 0.395 Chirality : 0.037 0.297 4288 Planarity : 0.005 0.069 2404 Dihedral : 22.494 178.786 12632 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.83 % Allowed : 7.79 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.65 (0.17), residues: 1344 helix: -4.88 (0.07), residues: 512 sheet: -0.44 (0.36), residues: 190 loop : -2.25 (0.19), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 22 HIS 0.003 0.001 HIS J 60 PHE 0.012 0.001 PHE D 152 TYR 0.019 0.002 TYR B 46 ARG 0.007 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7499 (mp0) cc_final: 0.7028 (mp0) REVERT: A 49 TRP cc_start: 0.7122 (t60) cc_final: 0.5839 (m-90) REVERT: A 79 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8356 (tttt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1753 time to fit residues: 8.5115 Evaluate side-chains 26 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.148 Evaluate side-chains 72 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 TYR cc_start: 0.6726 (p90) cc_final: 0.6084 (p90) REVERT: C 62 GLU cc_start: 0.6451 (mp0) cc_final: 0.5298 (tm-30) outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.2275 time to fit residues: 17.3787 Evaluate side-chains 46 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.245 Evaluate side-chains 29 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 LEU cc_start: 0.7892 (mt) cc_final: 0.7444 (mp) REVERT: E 42 LEU cc_start: 0.8314 (mt) cc_final: 0.7911 (mt) REVERT: E 62 LEU cc_start: 0.8204 (tt) cc_final: 0.7806 (mt) outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.3248 time to fit residues: 9.4486 Evaluate side-chains 17 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.099 Evaluate side-chains 46 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 49 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8317 (tmtt) REVERT: G 106 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8345 (mt-10) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2807 time to fit residues: 13.5224 Evaluate side-chains 32 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.135 Evaluate side-chains 20 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: I 45 LEU cc_start: 0.8017 (mt) cc_final: 0.7784 (mt) REVERT: I 80 ASP cc_start: 0.8690 (t70) cc_final: 0.8485 (p0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1783 time to fit residues: 3.8965 Evaluate side-chains 10 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.114 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.157 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1920 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 0.3980 chunk 92 optimal weight: 0.0040 chunk 72 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 overall best weight: 1.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN D 125 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23772 Z= 0.177 Angle : 0.611 9.023 34570 Z= 0.312 Chirality : 0.034 0.165 4288 Planarity : 0.005 0.052 2404 Dihedral : 23.442 178.822 9632 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.91 (0.19), residues: 1344 helix: -2.84 (0.15), residues: 528 sheet: 0.07 (0.38), residues: 196 loop : -1.64 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 120 HIS 0.007 0.001 HIS E 10 PHE 0.014 0.002 PHE G 4 TYR 0.025 0.002 TYR E 95 ARG 0.011 0.001 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: B 37 LEU cc_start: 0.9129 (pp) cc_final: 0.8383 (mp) REVERT: B 79 LYS cc_start: 0.8973 (ttmt) cc_final: 0.8542 (tttt) REVERT: B 83 ILE cc_start: 0.8732 (pt) cc_final: 0.8280 (mt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1068 time to fit residues: 3.9149 Evaluate side-chains 23 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.116 Evaluate side-chains 44 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 PHE cc_start: 0.8390 (m-10) cc_final: 0.8112 (m-10) REVERT: D 214 LEU cc_start: 0.8988 (tp) cc_final: 0.8635 (pp) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.2024 time to fit residues: 9.6957 Evaluate side-chains 30 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.226 Evaluate side-chains 19 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 LEU cc_start: 0.7766 (mt) cc_final: 0.7223 (mp) REVERT: F 42 LEU cc_start: 0.8106 (mt) cc_final: 0.7837 (mt) REVERT: F 90 LYS cc_start: 0.7072 (tptt) cc_final: 0.6638 (tptp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.3112 time to fit residues: 6.2068 Evaluate side-chains 10 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.097 Evaluate side-chains 34 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.120 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1553 time to fit residues: 5.7566 Evaluate side-chains 28 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.124 Evaluate side-chains 14 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.8263 (mt) cc_final: 0.7978 (mt) REVERT: J 80 ASP cc_start: 0.8959 (t70) cc_final: 0.8661 (t0) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1430 time to fit residues: 2.2702 Evaluate side-chains 8 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.097 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.161 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1998 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 chunk 176 optimal weight: 0.8980 chunk 145 optimal weight: 20.0000 chunk 162 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 174 ASN D 180 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 79 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23772 Z= 0.189 Angle : 0.770 23.296 34570 Z= 0.375 Chirality : 0.045 0.620 4288 Planarity : 0.008 0.106 2404 Dihedral : 23.386 178.915 9632 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 1.49 % Allowed : 5.97 % Favored : 92.54 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.46 (0.20), residues: 1344 helix: -1.90 (0.19), residues: 508 sheet: -0.41 (0.36), residues: 204 loop : -1.73 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.007 TRP A 57 HIS 0.033 0.004 HIS C 79 PHE 0.105 0.007 PHE A 63 TYR 0.099 0.007 TYR A 45 ARG 0.091 0.003 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8101 (tttt) REVERT: B 121 PHE cc_start: 0.3778 (t80) cc_final: 0.3496 (t80) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 0.1071 time to fit residues: 3.8158 Evaluate side-chains 19 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.131 Evaluate side-chains 43 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 PHE cc_start: 0.7958 (m-80) cc_final: 0.7650 (m-80) REVERT: D 214 LEU cc_start: 0.9031 (tp) cc_final: 0.8604 (pp) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1839 time to fit residues: 8.9258 Evaluate side-chains 29 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.210 Evaluate side-chains 18 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 LEU cc_start: 0.8113 (mt) cc_final: 0.7195 (mp) REVERT: E 42 LEU cc_start: 0.8381 (mt) cc_final: 0.8090 (mt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.2257 time to fit residues: 4.3326 Evaluate side-chains 12 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.099 Evaluate side-chains 30 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.129 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1340 time to fit residues: 4.4633 Evaluate side-chains 27 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.133 Evaluate side-chains 11 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.8281 (mt) cc_final: 0.8003 (mt) REVERT: J 80 ASP cc_start: 0.8945 (t70) cc_final: 0.8673 (t0) outliers start: 1 outliers final: 0 residues processed: 11 average time/residue: 0.1178 time to fit residues: 1.5318 Evaluate side-chains 8 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.094 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.125 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1636 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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: 68.6129 > 50: distance: 0 - 2: 3.824 distance: 1 - 3: 7.701 distance: 2 - 3: 5.832 distance: 4 - 5: 9.997 distance: 5 - 6: 37.674 distance: 5 - 8: 6.837 distance: 6 - 7: 19.300 distance: 6 - 12: 30.626 distance: 8 - 9: 32.113 distance: 8 - 10: 19.766 distance: 9 - 11: 19.975 distance: 12 - 13: 41.405 distance: 13 - 14: 39.548 distance: 13 - 16: 55.925 distance: 14 - 15: 26.486 distance: 14 - 20: 48.276 distance: 16 - 17: 28.600 distance: 16 - 18: 39.235 distance: 17 - 19: 17.211 distance: 20 - 21: 20.880 distance: 21 - 22: 9.012 distance: 21 - 24: 31.902 distance: 22 - 23: 31.850 distance: 22 - 28: 21.302 distance: 24 - 25: 21.577 distance: 25 - 26: 14.742 distance: 25 - 27: 11.067 distance: 28 - 29: 11.454 distance: 29 - 30: 52.646 distance: 29 - 32: 7.708 distance: 30 - 31: 25.139 distance: 30 - 36: 28.979 distance: 32 - 33: 30.250 distance: 32 - 34: 28.371 distance: 33 - 35: 28.121 distance: 36 - 37: 13.602 distance: 37 - 38: 40.975 distance: 37 - 40: 33.432 distance: 38 - 39: 41.965 distance: 38 - 45: 43.150 distance: 40 - 41: 34.197 distance: 41 - 42: 40.388 distance: 42 - 43: 24.357 distance: 42 - 44: 15.680 distance: 45 - 46: 46.429 distance: 46 - 47: 48.208 distance: 47 - 48: 7.975 distance: 47 - 49: 47.154 distance: 49 - 50: 5.858 distance: 50 - 51: 20.718 distance: 51 - 52: 23.398 distance: 51 - 53: 15.601 distance: 53 - 54: 32.187 distance: 54 - 55: 28.079 distance: 54 - 57: 41.270 distance: 55 - 56: 26.561 distance: 55 - 60: 11.939 distance: 56 - 85: 27.577 distance: 57 - 58: 37.298 distance: 57 - 59: 37.014 distance: 60 - 61: 8.956 distance: 61 - 62: 7.560 distance: 61 - 64: 22.992 distance: 62 - 63: 4.172 distance: 62 - 68: 15.910 distance: 64 - 65: 47.898 distance: 65 - 66: 37.796 distance: 65 - 67: 22.003 distance: 68 - 69: 30.271 distance: 69 - 70: 19.409 distance: 69 - 72: 43.545 distance: 70 - 71: 35.085 distance: 70 - 77: 21.716 distance: 72 - 73: 30.978 distance: 73 - 74: 9.138 distance: 74 - 75: 19.671 distance: 75 - 76: 28.469 distance: 77 - 78: 20.478 distance: 78 - 79: 16.074 distance: 78 - 81: 27.490 distance: 79 - 80: 22.925 distance: 79 - 85: 5.677 distance: 81 - 82: 8.357 distance: 81 - 83: 32.599 distance: 82 - 84: 13.361 distance: 85 - 86: 4.253 distance: 86 - 87: 8.418