Starting phenix.real_space_refine on Thu Aug 8 05:02:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/08_2024/6k0a_30036.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/08_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_30036/08_2024/6k0a_30036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/08_2024/6k0a_30036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/08_2024/6k0a_30036.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/08_2024/6k0a_30036.cif" } 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-5409/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: 13.61, per 1000 atoms: 0.61 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: 10.65 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: 11.66 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: 9.14 Time building geometry restraints manager: 11.61 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 3.040 nonbonded pdb=" OH TYR J 4 " pdb=" O ALA J 49 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR I 4 " pdb=" O ALA I 49 " model vdw 2.329 3.040 nonbonded pdb=" OP2 G Y 76 " pdb=" O2' A Y 252 " model vdw 2.359 3.040 nonbonded pdb=" OP2 G X 76 " pdb=" O2' A X 252 " model vdw 2.360 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 4.720 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: 0.030 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 77.030 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.560 ------------------------------------------------------------------------------- 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 : 0.128 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: 0.1695 time to fit residues: 8.2161 Evaluate side-chains 26 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.128 Evaluate side-chains 72 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.228 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: 0.2212 time to fit residues: 16.8600 Evaluate side-chains 46 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.230 Evaluate side-chains 29 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.096 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: 0.3141 time to fit residues: 9.1171 Evaluate side-chains 17 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.087 Evaluate side-chains 46 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.118 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: 0.2778 time to fit residues: 13.3605 Evaluate side-chains 32 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.119 Evaluate side-chains 20 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.094 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: 0.1679 time to fit residues: 3.6707 Evaluate side-chains 10 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.094 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.147 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1833 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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: 0.9980 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.0010 chunk 72 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 0.0030 chunk 163 optimal weight: 10.0000 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 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 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: 0.6237 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23772 Z= 0.181 Angle : 0.616 7.842 34570 Z= 0.313 Chirality : 0.035 0.168 4288 Planarity : 0.006 0.065 2404 Dihedral : 23.399 179.479 9632 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.36 % 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: -2.92 (0.20), residues: 1344 helix: -2.81 (0.15), residues: 528 sheet: 0.03 (0.38), residues: 196 loop : -1.66 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 120 HIS 0.008 0.001 HIS E 10 PHE 0.017 0.002 PHE D 210 TYR 0.042 0.003 TYR E 95 ARG 0.011 0.001 ARG D 153 *********************** 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 35 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.9113 (pp) cc_final: 0.8330 (mp) REVERT: B 49 TRP cc_start: 0.7051 (t60) cc_final: 0.5386 (m-90) REVERT: B 62 ASP cc_start: 0.2762 (p0) cc_final: 0.2508 (p0) REVERT: B 79 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8571 (tttt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1068 time to fit residues: 4.2744 Evaluate side-chains 24 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.133 Evaluate side-chains 43 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 214 LEU cc_start: 0.8939 (tp) cc_final: 0.8635 (pp) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.2372 time to fit residues: 10.9931 Evaluate side-chains 29 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.222 Evaluate side-chains 19 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 LEU cc_start: 0.7760 (mt) cc_final: 0.7108 (mp) REVERT: F 42 LEU cc_start: 0.8090 (mt) cc_final: 0.7789 (mt) REVERT: F 90 LYS cc_start: 0.7065 (tptt) cc_final: 0.6767 (tptp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2932 time to fit residues: 5.8473 Evaluate side-chains 11 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.096 Evaluate side-chains 36 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8011 (mpp80) cc_final: 0.7779 (ptt180) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1726 time to fit residues: 6.7148 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 Evaluate side-chains 14 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.8236 (mt) cc_final: 0.7965 (mt) REVERT: J 80 ASP cc_start: 0.8959 (t70) cc_final: 0.8675 (t0) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1399 time to fit residues: 2.2240 Evaluate side-chains 8 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.105 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.159 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2010 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 145 optimal weight: 50.0000 chunk 162 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 0.0050 overall best weight: 1.5800 ------------------------------------------------------------------------------- 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 180 ASN 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... 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23772 Z= 0.228 Angle : 0.787 21.395 34570 Z= 0.389 Chirality : 0.050 1.161 4288 Planarity : 0.009 0.157 2404 Dihedral : 23.392 179.869 9632 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.00 % Allowed : 6.80 % Favored : 92.21 % Cbeta Deviations : 0.00 % 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: -2.39 (0.20), residues: 1344 helix: -1.90 (0.19), residues: 514 sheet: -0.05 (0.36), residues: 198 loop : -1.74 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.008 TRP B 57 HIS 0.033 0.005 HIS C 79 PHE 0.103 0.008 PHE B 63 TYR 0.103 0.007 TYR A 65 ARG 0.093 0.003 ARG A 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: 4 poor density : 29 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8380 (tttt) REVERT: B 87 GLU cc_start: 0.8712 (tt0) cc_final: 0.7993 (mm-30) REVERT: B 121 PHE cc_start: 0.3388 (t80) cc_final: 0.3180 (t80) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.1282 time to fit residues: 4.4488 Evaluate side-chains 21 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.127 Evaluate side-chains 41 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 PHE cc_start: 0.8035 (m-80) cc_final: 0.7645 (m-80) REVERT: D 180 ASN cc_start: 0.7018 (m-40) cc_final: 0.6721 (m-40) REVERT: D 214 LEU cc_start: 0.9052 (tp) cc_final: 0.8557 (pp) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.2137 time to fit residues: 9.8024 Evaluate side-chains 29 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.220 Evaluate side-chains 20 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 LEU cc_start: 0.7986 (mt) cc_final: 0.7108 (mp) REVERT: E 42 LEU cc_start: 0.8338 (mt) cc_final: 0.8097 (mt) REVERT: E 95 TYR cc_start: 0.6305 (m-80) cc_final: 0.6062 (m-80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2350 time to fit residues: 4.9810 Evaluate side-chains 13 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.092 Evaluate side-chains 30 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 MET cc_start: 0.8719 (tmm) cc_final: 0.8175 (tmm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1579 time to fit residues: 5.1886 Evaluate side-chains 28 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.131 Evaluate side-chains 10 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.8291 (mt) cc_final: 0.8004 (mt) outliers start: 1 outliers final: 0 residues processed: 10 average time/residue: 0.1222 time to fit residues: 1.4588 Evaluate side-chains 7 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 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 : 0.163 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1990 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 109 optimal weight: 0.0170 chunk 164 optimal weight: 0.6980 chunk 173 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** 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 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... 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23772 Z= 0.220 Angle : 0.776 15.874 34570 Z= 0.389 Chirality : 0.050 0.920 4288 Planarity : 0.009 0.096 2404 Dihedral : 23.322 177.450 9632 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.85 % Favored : 93.01 % Rotamer: Outliers : 1.00 % Allowed : 5.14 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.07 (0.21), residues: 1344 helix: -1.02 (0.22), residues: 498 sheet: -0.52 (0.33), residues: 222 loop : -1.95 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.008 TRP A 120 HIS 0.019 0.003 HIS D 79 PHE 0.167 0.010 PHE B 63 TYR 0.104 0.007 TYR A 45 ARG 0.097 0.003 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 4 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 37 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9270 (mt) cc_final: 0.9066 (mm) REVERT: A 48 SER cc_start: 0.7617 (p) cc_final: 0.7248 (t) REVERT: A 87 GLU cc_start: 0.8580 (tt0) cc_final: 0.7974 (mp0) outliers start: 5 outliers final: 1 residues processed: 36 average time/residue: 0.1270 time to fit residues: 5.0975 Evaluate side-chains 20 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.134 Evaluate side-chains 42 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 74 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8582 (p90) REVERT: D 152 PHE cc_start: 0.8275 (m-80) cc_final: 0.8002 (m-80) REVERT: D 209 ASP cc_start: 0.7921 (m-30) cc_final: 0.7228 (m-30) REVERT: D 214 LEU cc_start: 0.9098 (tp) cc_final: 0.8790 (tt) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.2108 time to fit residues: 9.9010 Evaluate side-chains 27 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.202 Evaluate side-chains 13 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: E 42 LEU cc_start: 0.8423 (mt) cc_final: 0.8192 (mt) REVERT: E 95 TYR cc_start: 0.6464 (m-80) cc_final: 0.6141 (m-80) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1989 time to fit residues: 2.8388 Evaluate side-chains 7 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.111 Evaluate side-chains 30 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.145 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1595 time to fit residues: 5.2767 Evaluate side-chains 22 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.128 Evaluate side-chains 10 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.8416 (mt) cc_final: 0.8160 (mt) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.1105 time to fit residues: 1.3511 Evaluate side-chains 7 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.107 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.178 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2243 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 0.0670 chunk 71 optimal weight: 0.3980 chunk 148 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 0.0770 chunk 88 optimal weight: 0.4980 chunk 156 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 overall best weight: 0.2274 ------------------------------------------------------------------------------- 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... 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... 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 23772 Z= 0.286 Angle : 0.852 16.741 34570 Z= 0.420 Chirality : 0.081 2.989 4288 Planarity : 0.016 0.446 2404 Dihedral : 23.342 177.511 9632 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.59 % Favored : 92.11 % Rotamer: Outliers : 1.00 % Allowed : 4.64 % Favored : 94.36 % Cbeta Deviations : 0.00 % 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: -2.18 (0.21), residues: 1344 helix: -1.13 (0.21), residues: 512 sheet: -0.60 (0.35), residues: 202 loop : -1.96 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.008 TRP B 120 HIS 0.026 0.003 HIS D 79 PHE 0.120 0.009 PHE A 63 TYR 0.104 0.007 TYR A 45 ARG 0.093 0.003 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 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: 4 poor density : 29 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.8145 (ppp) cc_final: 0.7859 (tpt) REVERT: A 48 SER cc_start: 0.7633 (p) cc_final: 0.7142 (t) REVERT: A 87 GLU cc_start: 0.8576 (tt0) cc_final: 0.8007 (mp0) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.1311 time to fit residues: 4.5664 Evaluate side-chains 19 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.134 Evaluate side-chains 39 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 PHE cc_start: 0.8193 (m-80) cc_final: 0.7908 (m-80) REVERT: D 209 ASP cc_start: 0.7902 (m-30) cc_final: 0.7238 (m-30) REVERT: D 214 LEU cc_start: 0.9086 (tp) cc_final: 0.8678 (pp) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1925 time to fit residues: 8.4536 Evaluate side-chains 31 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.236 Evaluate side-chains 15 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: E 42 LEU cc_start: 0.8408 (mt) cc_final: 0.8185 (mt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1554 time to fit residues: 2.5822 Evaluate side-chains 7 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.095 Evaluate side-chains 24 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.131 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1143 time to fit residues: 3.1469 Evaluate side-chains 20 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.129 Evaluate side-chains 11 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 45 LEU cc_start: 0.8402 (mt) cc_final: 0.8151 (mt) outliers start: 1 outliers final: 1 residues processed: 11 average time/residue: 0.1104 time to fit residues: 1.4572 Evaluate side-chains 9 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.105 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: 0.2000 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 7.9990 chunk 156 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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... 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... 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23772 Z= 0.228 Angle : 0.797 13.783 34570 Z= 0.397 Chirality : 0.053 1.029 4288 Planarity : 0.009 0.118 2404 Dihedral : 23.324 177.543 9632 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.74 % Favored : 91.96 % Rotamer: Outliers : 0.17 % Allowed : 3.65 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.37 (0.21), residues: 1344 helix: -1.27 (0.21), residues: 516 sheet: -0.62 (0.33), residues: 222 loop : -2.15 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.008 TRP A 57 HIS 0.025 0.003 HIS D 79 PHE 0.086 0.008 PHE A 63 TYR 0.101 0.007 TYR A 45 ARG 0.123 0.003 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.139 Fit side-chains REVERT: A 48 SER cc_start: 0.7499 (p) cc_final: 0.6976 (t) REVERT: A 104 ILE cc_start: 0.8204 (mm) cc_final: 0.7809 (pt) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.1121 time to fit residues: 3.6102 Evaluate side-chains 20 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.143 Evaluate side-chains 42 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 PHE cc_start: 0.8206 (m-80) cc_final: 0.7971 (m-80) REVERT: D 209 ASP cc_start: 0.7906 (m-30) cc_final: 0.7219 (m-30) REVERT: D 214 LEU cc_start: 0.9107 (tp) cc_final: 0.8768 (tt) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1846 time to fit residues: 8.7430 Evaluate side-chains 28 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.212 Evaluate side-chains 14 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 21 GLU cc_start: 0.8181 (mp0) cc_final: 0.7971 (mp0) REVERT: E 42 LEU cc_start: 0.8374 (mt) cc_final: 0.8121 (mt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1361 time to fit residues: 2.1606 Evaluate side-chains 8 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.086 Evaluate side-chains 22 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.131 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0826 time to fit residues: 2.2333 Evaluate side-chains 19 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.134 Evaluate side-chains 9 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.8401 (mt) cc_final: 0.8132 (mt) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1210 time to fit residues: 1.3282 Evaluate side-chains 7 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.120 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.155 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1824 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 127 optimal weight: 30.0000 chunk 98 optimal weight: 7.9990 chunk 146 optimal weight: 0.0010 chunk 97 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 overall best weight: 3.2592 ------------------------------------------------------------------------------- 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... 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... 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 23772 Z= 0.311 Angle : 0.884 19.812 34570 Z= 0.437 Chirality : 0.053 0.922 4288 Planarity : 0.013 0.344 2404 Dihedral : 23.308 177.444 9632 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.89 % Favored : 91.67 % Rotamer: Outliers : 0.17 % Allowed : 2.32 % Favored : 97.51 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -2.39 (0.21), residues: 1344 helix: -1.28 (0.20), residues: 516 sheet: -0.67 (0.33), residues: 222 loop : -2.17 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.009 TRP A 120 HIS 0.019 0.003 HIS D 79 PHE 0.081 0.008 PHE A 88 TYR 0.103 0.006 TYR A 45 ARG 0.161 0.004 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.136 Fit side-chains REVERT: A 5 LEU cc_start: 0.7969 (mm) cc_final: 0.7662 (mm) REVERT: A 73 ASP cc_start: 0.8597 (m-30) cc_final: 0.8106 (t70) REVERT: A 104 ILE cc_start: 0.8287 (mm) cc_final: 0.7941 (pt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0838 time to fit residues: 2.5278 Evaluate side-chains 18 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.116 Evaluate side-chains 38 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 PHE cc_start: 0.8269 (m-80) cc_final: 0.8054 (m-80) REVERT: D 214 LEU cc_start: 0.9086 (tp) cc_final: 0.8688 (pp) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.1600 time to fit residues: 6.8152 Evaluate side-chains 28 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.206 Evaluate side-chains 14 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: E 42 LEU cc_start: 0.8385 (mt) cc_final: 0.8159 (mt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1320 time to fit residues: 2.0946 Evaluate side-chains 6 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.096 Evaluate side-chains 22 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.120 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0816 time to fit residues: 2.1888 Evaluate side-chains 19 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.118 Evaluate side-chains 9 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: J 45 LEU cc_start: 0.8447 (mt) cc_final: 0.8197 (mt) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1099 time to fit residues: 1.2035 Evaluate side-chains 7 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.108 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.162 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2201 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) 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 400, 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 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-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/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-5409/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-5409/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-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: 52.9082 > 50: distance: 0 - 1: 15.838 distance: 0 - 6: 5.744 distance: 6 - 7: 7.902 distance: 7 - 8: 18.012 distance: 7 - 10: 11.714 distance: 8 - 9: 23.345 distance: 8 - 17: 6.096 distance: 10 - 11: 9.725 distance: 11 - 12: 26.574 distance: 12 - 13: 3.388 distance: 13 - 14: 7.409 distance: 14 - 15: 8.148 distance: 14 - 16: 7.956 distance: 17 - 18: 12.676 distance: 18 - 19: 10.865 distance: 19 - 20: 15.255 distance: 19 - 26: 5.425 distance: 21 - 22: 21.907 distance: 22 - 23: 22.534 distance: 23 - 24: 12.608 distance: 23 - 25: 16.721 distance: 26 - 27: 5.032 distance: 27 - 28: 13.393 distance: 27 - 30: 5.079 distance: 28 - 35: 15.345 distance: 30 - 31: 6.674 distance: 31 - 32: 3.994 distance: 32 - 33: 4.977 distance: 33 - 34: 7.081 distance: 35 - 36: 20.318 distance: 36 - 37: 17.402 distance: 36 - 39: 15.764 distance: 37 - 38: 16.738 distance: 37 - 44: 5.149 distance: 39 - 40: 8.741 distance: 40 - 41: 7.811 distance: 42 - 43: 7.874 distance: 44 - 45: 15.557 distance: 45 - 46: 11.682 distance: 45 - 48: 10.100 distance: 46 - 47: 22.853 distance: 46 - 55: 13.853 distance: 48 - 49: 27.795 distance: 49 - 50: 18.098 distance: 50 - 51: 6.933 distance: 52 - 53: 10.263 distance: 52 - 54: 8.571 distance: 55 - 56: 24.673 distance: 56 - 57: 23.303 distance: 56 - 59: 30.715 distance: 57 - 58: 13.144 distance: 57 - 67: 33.396 distance: 59 - 60: 28.483 distance: 60 - 61: 19.898 distance: 60 - 62: 29.149 distance: 61 - 63: 11.204 distance: 62 - 64: 10.314 distance: 63 - 65: 10.919 distance: 64 - 65: 17.072 distance: 65 - 66: 9.248 distance: 67 - 68: 23.346 distance: 68 - 69: 7.372 distance: 68 - 71: 16.878 distance: 69 - 70: 27.519 distance: 69 - 75: 11.373 distance: 71 - 72: 30.010 distance: 71 - 73: 31.125 distance: 72 - 74: 52.528 distance: 75 - 76: 7.579 distance: 76 - 77: 8.679 distance: 76 - 79: 13.454 distance: 77 - 78: 8.808 distance: 77 - 80: 3.357 distance: 80 - 81: 3.589 distance: 81 - 82: 9.526 distance: 81 - 84: 4.309 distance: 82 - 83: 16.769