Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 17 04:47:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wto_32793/05_2023/7wto_32793.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wto_32793/05_2023/7wto_32793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wto_32793/05_2023/7wto_32793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wto_32793/05_2023/7wto_32793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wto_32793/05_2023/7wto_32793.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wto_32793/05_2023/7wto_32793.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 1 6.06 5 P 1200 5.49 5 S 36 5.16 5 C 23398 2.51 5 N 8131 2.21 5 O 11724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "SB ASP 31": "OD1" <-> "OD2" Residue "SB ASP 72": "OD1" <-> "OD2" Residue "SB PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB GLU 90": "OE1" <-> "OE2" Residue "SB TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB GLU 191": "OE1" <-> "OE2" Residue "SB PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE ASP 93": "OD1" <-> "OD2" Residue "SE GLU 97": "OE1" <-> "OE2" Residue "SE TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE GLU 230": "OE1" <-> "OE2" Residue "SE GLU 250": "OE1" <-> "OE2" Residue "SG TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG GLU 17": "OE1" <-> "OE2" Residue "SG PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH GLU 26": "OE1" <-> "OE2" Residue "SH PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH GLU 134": "OE1" <-> "OE2" Residue "SH TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI GLU 61": "OE1" <-> "OE2" Residue "SI GLU 114": "OE1" <-> "OE2" Residue "SI TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI GLU 140": "OE1" <-> "OE2" Residue "SI GLU 157": "OE1" <-> "OE2" Residue "SI PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI GLU 185": "OE1" <-> "OE2" Residue "SI GLU 187": "OE1" <-> "OE2" Residue "SI GLU 188": "OE1" <-> "OE2" Residue "SI TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ GLU 27": "OE1" <-> "OE2" Residue "SJ TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ ASP 66": "OD1" <-> "OD2" Residue "SJ GLU 88": "OE1" <-> "OE2" Residue "SJ ASP 89": "OD1" <-> "OD2" Residue "SJ GLU 102": "OE1" <-> "OE2" Residue "SJ ASP 103": "OD1" <-> "OD2" Residue "SJ GLU 182": "OE1" <-> "OE2" Residue "SL GLU 10": "OE1" <-> "OE2" Residue "SN ASP 56": "OD1" <-> "OD2" Residue "SN GLU 86": "OE1" <-> "OE2" Residue "SN GLU 142": "OE1" <-> "OE2" Residue "SW ASP 55": "OD1" <-> "OD2" Residue "SW GLU 87": "OE1" <-> "OE2" Residue "SW GLU 114": "OE1" <-> "OE2" Residue "SX GLU 98": "OE1" <-> "OE2" Residue "SY PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY GLU 39": "OE1" <-> "OE2" Residue "SY GLU 46": "OE1" <-> "OE2" Residue "SY TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY GLU 98": "OE1" <-> "OE2" Residue "SY PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Sb GLU 15": "OE1" <-> "OE2" Residue "Sb PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Se TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA ASP 179": "OD1" <-> "OD2" Residue "CA PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA ASP 189": "OD1" <-> "OD2" Residue "CA PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 44490 Number of models: 1 Model: "" Number of chains: 17 Chain: "C2" Number of atoms: 25592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1200, 25592 Classifications: {'RNA': 1200} Modifications used: {'rna2p_pur': 100, 'rna2p_pyr': 86, 'rna3p_pur': 548, 'rna3p_pyr': 466} Link IDs: {'rna2p': 186, 'rna3p': 1013} Chain breaks: 9 Chain: "SB" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1722 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "SE" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "SG" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1755 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain: "SH" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1486 Classifications: {'peptide': 185} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 171} Chain: "SI" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "SJ" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "SL" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1168 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "SN" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "SO" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 949 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "SW" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "SX" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "SY" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Sb" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "Se" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 313 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "CA" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain: "Sb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.27, per 1000 atoms: 0.52 Number of scatterers: 44490 At special positions: 0 Unit cell: (167.322, 225.567, 172.617, 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 1 29.99 S 36 16.00 P 1200 15.00 O 11724 8.00 N 8131 7.00 C 23398 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: 22.85 Conformation dependent library (CDL) restraints added in 3.0 seconds 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 25 sheets defined 35.3% alpha, 17.9% beta 398 base pairs and 630 stacking pairs defined. Time for finding SS restraints: 17.01 Creating SS restraints... Processing helix chain 'SB' and resid 22 through 26 Processing helix chain 'SB' and resid 70 through 75 Processing helix chain 'SB' and resid 76 through 80 removed outlier: 3.953A pdb=" N HISSB 79 " --> pdb=" O SERSB 76 " (cutoff:3.500A) Processing helix chain 'SB' and resid 106 through 114 Processing helix chain 'SB' and resid 157 through 178 removed outlier: 3.910A pdb=" N GLYSB 178 " --> pdb=" O LYSSB 174 " (cutoff:3.500A) Processing helix chain 'SB' and resid 180 through 189 Processing helix chain 'SB' and resid 191 through 202 removed outlier: 4.010A pdb=" N LYSSB 195 " --> pdb=" O GLUSB 191 " (cutoff:3.500A) Processing helix chain 'SB' and resid 224 through 232 removed outlier: 3.808A pdb=" N LEUSB 228 " --> pdb=" O ASPSB 224 " (cutoff:3.500A) Processing helix chain 'SE' and resid 15 through 19 Processing helix chain 'SE' and resid 37 through 41 removed outlier: 3.536A pdb=" N SERSE 41 " --> pdb=" O LEUSE 38 " (cutoff:3.500A) Processing helix chain 'SE' and resid 44 through 50 Processing helix chain 'SE' and resid 57 through 66 Processing helix chain 'SE' and resid 133 through 135 No H-bonds generated for 'chain 'SE' and resid 133 through 135' Processing helix chain 'SE' and resid 247 through 259 Processing helix chain 'SG' and resid 21 through 25 removed outlier: 3.503A pdb=" N ARGSG 25 " --> pdb=" O HISSG 22 " (cutoff:3.500A) Processing helix chain 'SG' and resid 137 through 146 Processing helix chain 'SG' and resid 152 through 156 Processing helix chain 'SG' and resid 180 through 216 Processing helix chain 'SH' and resid 14 through 29 Processing helix chain 'SH' and resid 31 through 39 removed outlier: 3.662A pdb=" N ARGSH 39 " --> pdb=" O LYSSH 35 " (cutoff:3.500A) Processing helix chain 'SH' and resid 66 through 74 removed outlier: 4.135A pdb=" N PHESH 70 " --> pdb=" O SERSH 66 " (cutoff:3.500A) Processing helix chain 'SH' and resid 75 through 85 Processing helix chain 'SH' and resid 113 through 116 Processing helix chain 'SH' and resid 117 through 130 removed outlier: 3.759A pdb=" N VALSH 121 " --> pdb=" O THRSH 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VALSH 130 " --> pdb=" O LEUSH 126 " (cutoff:3.500A) Processing helix chain 'SH' and resid 165 through 177 Processing helix chain 'SI' and resid 25 through 27 No H-bonds generated for 'chain 'SI' and resid 25 through 27' Processing helix chain 'SI' and resid 49 through 51 No H-bonds generated for 'chain 'SI' and resid 49 through 51' Processing helix chain 'SI' and resid 88 through 93 removed outlier: 3.960A pdb=" N ARGSI 92 " --> pdb=" O ASNSI 88 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THRSI 93 " --> pdb=" O GLUSI 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'SI' and resid 88 through 93' Processing helix chain 'SI' and resid 106 through 117 Processing helix chain 'SI' and resid 136 through 146 removed outlier: 3.935A pdb=" N GLUSI 140 " --> pdb=" O SERSI 136 " (cutoff:3.500A) Processing helix chain 'SI' and resid 153 through 163 removed outlier: 3.558A pdb=" N GLUSI 157 " --> pdb=" O GLUSI 153 " (cutoff:3.500A) Processing helix chain 'SI' and resid 172 through 177 Processing helix chain 'SI' and resid 185 through 200 removed outlier: 3.728A pdb=" N LEUSI 189 " --> pdb=" O GLUSI 185 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 20 through 35 Processing helix chain 'SJ' and resid 39 through 61 Processing helix chain 'SJ' and resid 66 through 84 Processing helix chain 'SJ' and resid 92 through 97 Processing helix chain 'SJ' and resid 100 through 106 removed outlier: 3.759A pdb=" N PHESJ 104 " --> pdb=" O LYSSJ 100 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 108 through 116 Processing helix chain 'SJ' and resid 121 through 131 removed outlier: 3.717A pdb=" N GLNSJ 131 " --> pdb=" O VALSJ 127 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 162 through 166 Processing helix chain 'SJ' and resid 170 through 184 Processing helix chain 'SL' and resid 45 through 50 removed outlier: 3.827A pdb=" N ILESL 49 " --> pdb=" O PROSL 45 " (cutoff:3.500A) Processing helix chain 'SN' and resid 31 through 44 Processing helix chain 'SN' and resid 46 through 58 Processing helix chain 'SN' and resid 62 through 68 removed outlier: 3.729A pdb=" N ILESN 66 " --> pdb=" O GLNSN 62 " (cutoff:3.500A) Processing helix chain 'SN' and resid 70 through 78 Processing helix chain 'SN' and resid 85 through 105 Processing helix chain 'SN' and resid 108 through 132 Processing helix chain 'SN' and resid 144 through 151 removed outlier: 4.039A pdb=" N ALASN 148 " --> pdb=" O ALASN 144 " (cutoff:3.500A) Processing helix chain 'SO' and resid 56 through 75 Processing helix chain 'SO' and resid 95 through 108 removed outlier: 3.611A pdb=" N GLNSO 99 " --> pdb=" O GLYSO 95 " (cutoff:3.500A) Processing helix chain 'SW' and resid 5 through 21 removed outlier: 3.591A pdb=" N ASPSW 9 " --> pdb=" O SERSW 5 " (cutoff:3.500A) Processing helix chain 'SW' and resid 31 through 44 Processing helix chain 'SW' and resid 82 through 84 No H-bonds generated for 'chain 'SW' and resid 82 through 84' Processing helix chain 'SW' and resid 85 through 94 Processing helix chain 'SW' and resid 113 through 119 Processing helix chain 'SX' and resid 11 through 25 removed outlier: 3.855A pdb=" N LEUSX 15 " --> pdb=" O SERSX 11 " (cutoff:3.500A) Processing helix chain 'SX' and resid 27 through 33 Processing helix chain 'SX' and resid 35 through 40 removed outlier: 3.687A pdb=" N LYSSX 39 " --> pdb=" O GLYSX 35 " (cutoff:3.500A) Processing helix chain 'SX' and resid 132 through 137 Processing helix chain 'SY' and resid 36 through 48 removed outlier: 4.108A pdb=" N TYRSY 48 " --> pdb=" O LEUSY 44 " (cutoff:3.500A) Processing helix chain 'SY' and resid 51 through 53 No H-bonds generated for 'chain 'SY' and resid 51 through 53' Processing helix chain 'SY' and resid 79 through 86 Processing helix chain 'SY' and resid 87 through 94 Processing helix chain 'SY' and resid 104 through 116 Processing helix chain 'SY' and resid 122 through 135 removed outlier: 4.097A pdb=" N ASPSY 135 " --> pdb=" O ARGSY 131 " (cutoff:3.500A) Processing helix chain 'Se' and resid 32 through 44 Processing helix chain 'CA' and resid 102 through 104 No H-bonds generated for 'chain 'CA' and resid 102 through 104' Processing helix chain 'CA' and resid 105 through 112 Processing helix chain 'CA' and resid 112 through 123 Proline residue: CA 118 - end of helix Processing helix chain 'CA' and resid 148 through 163 removed outlier: 3.879A pdb=" N LEUCA 152 " --> pdb=" O ASPCA 148 " (cutoff:3.500A) Processing helix chain 'CA' and resid 167 through 177 Processing helix chain 'CA' and resid 187 through 191 Processing helix chain 'CA' and resid 195 through 207 Processing helix chain 'CA' and resid 210 through 220 Processing helix chain 'CA' and resid 236 through 253 removed outlier: 3.692A pdb=" N GLYCA 253 " --> pdb=" O SERCA 249 " (cutoff:3.500A) Processing helix chain 'CA' and resid 255 through 272 removed outlier: 3.682A pdb=" N VALCA 259 " --> pdb=" O PROCA 255 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLUCA 272 " --> pdb=" O SERCA 268 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'SB' and resid 42 through 48 removed outlier: 8.331A pdb=" N LEUSB 96 " --> pdb=" O TRPSB 29 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASPSB 31 " --> pdb=" O LEUSB 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'SB' and resid 66 through 69 removed outlier: 8.444A pdb=" N HISSB 101 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHESB 105 " --> pdb=" O ARGSB 213 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N ARGSB 213 " --> pdb=" O PHESB 105 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASNSB 209 " --> pdb=" O PHESB 142 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHESB 142 " --> pdb=" O ASNSB 209 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHESB 138 " --> pdb=" O ARGSB 213 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VALSB 215 " --> pdb=" O ARGSB 136 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARGSB 136 " --> pdb=" O VALSB 215 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEUSB 217 " --> pdb=" O VALSB 134 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VALSB 134 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SE' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'SE' and resid 75 through 76 removed outlier: 4.031A pdb=" N ASNSE 98 " --> pdb=" O ILESE 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'SE' and resid 102 through 103 removed outlier: 4.335A pdb=" N VALSE 102 " --> pdb=" O ALASE 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'SE' and resid 146 through 148 Processing sheet with id=AA7, first strand: chain 'SE' and resid 218 through 221 removed outlier: 3.504A pdb=" N HISSE 197 " --> pdb=" O HISSE 209 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYSSE 211 " --> pdb=" O ILESE 195 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILESE 195 " --> pdb=" O LYSSE 211 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYSSE 179 " --> pdb=" O ILESE 195 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLYSE 229 " --> pdb=" O LEUSE 180 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYRSE 182 " --> pdb=" O VALSE 227 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VALSE 227 " --> pdb=" O TYRSE 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'SG' and resid 12 through 17 removed outlier: 6.354A pdb=" N LEUSG 106 " --> pdb=" O ASPSG 57 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASPSG 57 " --> pdb=" O LEUSG 106 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VALSG 108 " --> pdb=" O GLYSG 55 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLYSG 55 " --> pdb=" O VALSG 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALASG 110 " --> pdb=" O SERSG 53 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VALSG 49 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'SG' and resid 72 through 76 Processing sheet with id=AB1, first strand: chain 'SG' and resid 160 through 163 Processing sheet with id=AB2, first strand: chain 'SH' and resid 45 through 50 removed outlier: 6.681A pdb=" N LYSSH 56 " --> pdb=" O HISSH 89 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILESH 91 " --> pdb=" O LYSSH 56 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEUSH 58 " --> pdb=" O ILESH 91 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEUSH 93 " --> pdb=" O LEUSH 58 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILESH 60 " --> pdb=" O LEUSH 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'SH' and resid 181 through 184 removed outlier: 8.149A pdb=" N VALSH 182 " --> pdb=" O LYSSH 148 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLNSH 150 " --> pdb=" O VALSH 182 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLUSH 184 " --> pdb=" O GLNSH 150 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VALSH 152 " --> pdb=" O GLUSH 184 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYSSH 138 " --> pdb=" O ASPSW 54 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHESW 50 " --> pdb=" O TYRSH 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'SI' and resid 3 through 4 removed outlier: 3.888A pdb=" N ILESI 3 " --> pdb=" O GLYSI 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'SI' and resid 37 through 38 removed outlier: 6.204A pdb=" N LYSSI 37 " --> pdb=" O ILESI 60 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARGSI 42 " --> pdb=" O LEUSI 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'SI' and resid 72 through 75 removed outlier: 6.938A pdb=" N ASNSI 64 " --> pdb=" O GLYSI 181 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILESI 183 " --> pdb=" O ASNSI 64 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SERSI 66 " --> pdb=" O ILESI 183 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILESI 101 " --> pdb=" O VALSI 82 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASPSI 105 " --> pdb=" O ILESI 78 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILESI 78 " --> pdb=" O ASPSI 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'SJ' and resid 139 through 141 Processing sheet with id=AB8, first strand: chain 'SL' and resid 70 through 77 removed outlier: 16.880A pdb=" N LEUSL 71 " --> pdb=" O LEUSL 91 " (cutoff:3.500A) removed outlier: 15.658A pdb=" N LEUSL 91 " --> pdb=" O LEUSL 71 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLYSL 73 " --> pdb=" O ALASL 89 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALASL 89 " --> pdb=" O GLYSL 73 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VALSL 75 " --> pdb=" O ARGSL 87 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARGSL 87 " --> pdb=" O VALSL 75 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHESL 137 " --> pdb=" O PROSL 108 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VALSL 139 " --> pdb=" O GLYSL 126 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLYSL 126 " --> pdb=" O VALSL 139 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASPSL 121 " --> pdb=" O VALSL 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'SO' and resid 38 through 42 removed outlier: 6.499A pdb=" N GLYSO 15 " --> pdb=" O HISSO 80 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LYSSO 82 " --> pdb=" O GLYSO 15 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALASO 17 " --> pdb=" O LYSSO 82 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ARGSO 84 " --> pdb=" O ALASO 17 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILESO 19 " --> pdb=" O ARGSO 84 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VALSO 81 " --> pdb=" O GLYSO 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'SW' and resid 71 through 74 removed outlier: 5.408A pdb=" N ILESW 125 " --> pdb=" O THRSW 105 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THRSW 105 " --> pdb=" O ILESW 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SX' and resid 82 through 84 removed outlier: 3.565A pdb=" N CYSSX 71 " --> pdb=" O LEUSX 57 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLNSX 75 " --> pdb=" O VALSX 53 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VALSX 53 " --> pdb=" O GLNSX 75 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEUSX 103 " --> pdb=" O VALSX 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SY' and resid 6 through 15 removed outlier: 4.258A pdb=" N VALSY 12 " --> pdb=" O GLNSY 22 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLNSY 22 " --> pdb=" O VALSY 12 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SERSY 14 " --> pdb=" O ARGSY 20 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARGSY 20 " --> pdb=" O SERSY 14 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLYSY 67 " --> pdb=" O HISSY 29 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VALSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHESY 60 " --> pdb=" O VALSY 70 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHESY 72 " --> pdb=" O PHESY 58 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Sb' and resid 43 through 47 Processing sheet with id=AC5, first strand: chain 'Sb' and resid 64 through 65 Processing sheet with id=AC6, first strand: chain 'CA' and resid 95 through 100 Processing sheet with id=AC7, first strand: chain 'CA' and resid 181 through 186 768 hydrogen bonds defined for protein. 2151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 954 hydrogen bonds 1478 hydrogen bond angles 0 basepair planarities 398 basepair parallelities 630 stacking parallelities Total time for adding SS restraints: 35.29 Time building geometry restraints manager: 24.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6539 1.33 - 1.45: 18606 1.45 - 1.57: 20253 1.57 - 1.69: 2390 1.69 - 1.81: 56 Bond restraints: 47844 Sorted by residual: bond pdb=" C GLNSX 63 " pdb=" N PROSX 64 " ideal model delta sigma weight residual 1.334 1.398 -0.065 2.34e-02 1.83e+03 7.60e+00 bond pdb=" C PHESH 131 " pdb=" N PROSH 132 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.22e-02 6.72e+03 5.64e+00 bond pdb=" C THRSI 107 " pdb=" N PROSI 108 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.28e-02 6.10e+03 3.02e+00 bond pdb=" C3' UC2 272 " pdb=" O3' UC2 272 " ideal model delta sigma weight residual 1.427 1.452 -0.025 1.50e-02 4.44e+03 2.78e+00 bond pdb=" N ARGSW 68 " pdb=" CA ARGSW 68 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.60e+00 ... (remaining 47839 not shown) Histogram of bond angle deviations from ideal: 99.75 - 107.05: 7740 107.05 - 114.35: 29500 114.35 - 121.66: 21783 121.66 - 128.96: 10221 128.96 - 136.27: 1142 Bond angle restraints: 70386 Sorted by residual: angle pdb=" C SERSH 30 " pdb=" N SERSH 31 " pdb=" CA SERSH 31 " ideal model delta sigma weight residual 121.70 132.58 -10.88 1.80e+00 3.09e-01 3.65e+01 angle pdb=" CA LEUSG 69 " pdb=" CB LEUSG 69 " pdb=" CG LEUSG 69 " ideal model delta sigma weight residual 116.30 134.98 -18.68 3.50e+00 8.16e-02 2.85e+01 angle pdb=" C LYSSY 49 " pdb=" N ALASY 50 " pdb=" CA ALASY 50 " ideal model delta sigma weight residual 122.08 114.57 7.51 1.53e+00 4.27e-01 2.41e+01 angle pdb=" CA LYSSY 49 " pdb=" CB LYSSY 49 " pdb=" CG LYSSY 49 " ideal model delta sigma weight residual 114.10 123.51 -9.41 2.00e+00 2.50e-01 2.21e+01 angle pdb=" C3' UC2 272 " pdb=" O3' UC2 272 " pdb=" P GC2 273 " ideal model delta sigma weight residual 120.20 127.11 -6.91 1.50e+00 4.44e-01 2.12e+01 ... (remaining 70381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 25205 35.92 - 71.83: 951 71.83 - 107.75: 82 107.75 - 143.66: 10 143.66 - 179.58: 17 Dihedral angle restraints: 26265 sinusoidal: 19415 harmonic: 6850 Sorted by residual: dihedral pdb=" CA VALSH 64 " pdb=" C VALSH 64 " pdb=" N PROSH 65 " pdb=" CA PROSH 65 " ideal model delta harmonic sigma weight residual 180.00 132.57 47.43 0 5.00e+00 4.00e-02 9.00e+01 dihedral pdb=" O4' UC2 767 " pdb=" C1' UC2 767 " pdb=" N1 UC2 767 " pdb=" C2 UC2 767 " ideal model delta sinusoidal sigma weight residual 200.00 28.42 171.58 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" CA LEUSH 9 " pdb=" C LEUSH 9 " pdb=" N SERSH 10 " pdb=" CA SERSH 10 " ideal model delta harmonic sigma weight residual 180.00 134.62 45.38 0 5.00e+00 4.00e-02 8.24e+01 ... (remaining 26262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 7779 0.063 - 0.125: 913 0.125 - 0.188: 153 0.188 - 0.250: 28 0.250 - 0.313: 9 Chirality restraints: 8882 Sorted by residual: chirality pdb=" C1' UC2 861 " pdb=" O4' UC2 861 " pdb=" C2' UC2 861 " pdb=" N1 UC2 861 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C3' UC2 272 " pdb=" C4' UC2 272 " pdb=" O3' UC2 272 " pdb=" C2' UC2 272 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILESX 59 " pdb=" CA ILESX 59 " pdb=" CG1 ILESX 59 " pdb=" CG2 ILESX 59 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 8879 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CC2 962 " 0.024 2.00e-02 2.50e+03 3.19e-02 2.28e+01 pdb=" N1 CC2 962 " -0.024 2.00e-02 2.50e+03 pdb=" C2 CC2 962 " -0.075 2.00e-02 2.50e+03 pdb=" O2 CC2 962 " 0.046 2.00e-02 2.50e+03 pdb=" N3 CC2 962 " -0.001 2.00e-02 2.50e+03 pdb=" C4 CC2 962 " 0.000 2.00e-02 2.50e+03 pdb=" N4 CC2 962 " 0.015 2.00e-02 2.50e+03 pdb=" C5 CC2 962 " 0.010 2.00e-02 2.50e+03 pdb=" C6 CC2 962 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GC2 867 " 0.011 2.00e-02 2.50e+03 2.44e-02 1.79e+01 pdb=" N9 GC2 867 " -0.012 2.00e-02 2.50e+03 pdb=" C8 GC2 867 " -0.004 2.00e-02 2.50e+03 pdb=" N7 GC2 867 " -0.009 2.00e-02 2.50e+03 pdb=" C5 GC2 867 " -0.003 2.00e-02 2.50e+03 pdb=" C6 GC2 867 " 0.008 2.00e-02 2.50e+03 pdb=" O6 GC2 867 " -0.005 2.00e-02 2.50e+03 pdb=" N1 GC2 867 " 0.006 2.00e-02 2.50e+03 pdb=" C2 GC2 867 " 0.064 2.00e-02 2.50e+03 pdb=" N2 GC2 867 " -0.051 2.00e-02 2.50e+03 pdb=" N3 GC2 867 " -0.001 2.00e-02 2.50e+03 pdb=" C4 GC2 867 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CC2 224 " 0.010 2.00e-02 2.50e+03 2.70e-02 1.64e+01 pdb=" N1 CC2 224 " 0.002 2.00e-02 2.50e+03 pdb=" C2 CC2 224 " -0.067 2.00e-02 2.50e+03 pdb=" O2 CC2 224 " 0.037 2.00e-02 2.50e+03 pdb=" N3 CC2 224 " 0.007 2.00e-02 2.50e+03 pdb=" C4 CC2 224 " -0.015 2.00e-02 2.50e+03 pdb=" N4 CC2 224 " 0.015 2.00e-02 2.50e+03 pdb=" C5 CC2 224 " 0.013 2.00e-02 2.50e+03 pdb=" C6 CC2 224 " -0.002 2.00e-02 2.50e+03 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 2053 2.66 - 3.22: 36645 3.22 - 3.78: 82845 3.78 - 4.34: 108455 4.34 - 4.90: 151675 Nonbonded interactions: 381673 Sorted by model distance: nonbonded pdb=" O4 UC2 229 " pdb=" O6 GC2 235 " model vdw 2.105 3.040 nonbonded pdb=" O4 UC2 873 " pdb=" O6 GC2 954 " model vdw 2.114 3.040 nonbonded pdb=" O2' UC2 8 " pdb=" OP2 AC21139 " model vdw 2.189 2.440 nonbonded pdb=" OH TYRSY 76 " pdb=" OE2 GLUSY 86 " model vdw 2.205 2.440 nonbonded pdb=" O2 UC2 231 " pdb=" O6 GC2 234 " model vdw 2.221 3.040 ... (remaining 381668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 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: 13.550 Check model and map are aligned: 0.660 Set scattering table: 0.370 Process input model: 139.920 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.005 0.065 47844 Z= 0.302 Angle : 0.839 18.679 70386 Z= 0.428 Chirality : 0.044 0.313 8882 Planarity : 0.007 0.080 4494 Dihedral : 15.977 179.577 21843 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.87 % Favored : 92.05 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 3.06 % Twisted General : 0.13 % 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: -2.03 (0.16), residues: 2351 helix: -0.43 (0.18), residues: 739 sheet: -0.90 (0.24), residues: 454 loop : -2.17 (0.16), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 3.057 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.6282 time to fit residues: 388.0821 Evaluate side-chains 315 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.851 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 179 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 275 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 318 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 69 HIS SE 209 HIS ** SE 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 10 ASN SJ 48 GLN SN 58 HIS SN 101 HIS SN 105 ASN ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 127 GLN CA 218 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 47844 Z= 0.253 Angle : 0.628 13.356 70386 Z= 0.323 Chirality : 0.037 0.312 8882 Planarity : 0.005 0.069 4494 Dihedral : 15.453 178.660 17015 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.46 % Favored : 91.37 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 2.04 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.17), residues: 2351 helix: 0.40 (0.19), residues: 766 sheet: -0.72 (0.24), residues: 450 loop : -2.20 (0.17), residues: 1135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 335 time to evaluate : 3.870 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 351 average time/residue: 0.5773 time to fit residues: 333.1457 Evaluate side-chains 329 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 303 time to evaluate : 3.021 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4373 time to fit residues: 24.1126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 265 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 319 optimal weight: 0.4980 chunk 344 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 316 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 chunk 256 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 209 HIS ** SE 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 197 ASN SJ 48 GLN SN 105 ASN ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 19 HIS ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 47844 Z= 0.231 Angle : 0.605 11.704 70386 Z= 0.311 Chirality : 0.036 0.321 8882 Planarity : 0.005 0.066 4494 Dihedral : 15.392 179.947 17015 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.63 % Favored : 91.24 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 1.02 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2351 helix: 0.71 (0.19), residues: 766 sheet: -0.81 (0.23), residues: 467 loop : -2.14 (0.17), residues: 1118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 334 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 344 average time/residue: 0.5837 time to fit residues: 326.0343 Evaluate side-chains 336 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 321 time to evaluate : 3.078 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3990 time to fit residues: 14.8416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 52.0795 > 50: distance: 53 - 58: 6.487 distance: 58 - 59: 21.490 distance: 59 - 60: 28.261 distance: 59 - 62: 22.314 distance: 60 - 61: 35.428 distance: 60 - 65: 7.781 distance: 62 - 63: 4.285 distance: 62 - 64: 10.080 distance: 65 - 66: 22.538 distance: 66 - 67: 8.170 distance: 66 - 69: 9.923 distance: 67 - 68: 10.922 distance: 67 - 71: 5.871 distance: 68 - 89: 27.447 distance: 69 - 70: 22.692 distance: 71 - 72: 11.026 distance: 71 - 77: 10.843 distance: 72 - 73: 9.958 distance: 72 - 75: 9.877 distance: 73 - 74: 24.074 distance: 73 - 78: 5.020 distance: 74 - 93: 18.522 distance: 76 - 77: 11.834 distance: 78 - 79: 22.920 distance: 79 - 80: 16.604 distance: 79 - 82: 12.442 distance: 80 - 81: 20.283 distance: 82 - 83: 8.571 distance: 83 - 84: 7.959 distance: 83 - 85: 12.960 distance: 84 - 86: 8.649 distance: 85 - 87: 10.127 distance: 86 - 88: 14.450 distance: 87 - 88: 6.946 distance: 89 - 90: 16.159 distance: 90 - 91: 37.356 distance: 91 - 92: 23.603 distance: 91 - 93: 15.563 distance: 93 - 94: 5.774 distance: 94 - 95: 20.635 distance: 95 - 96: 22.443 distance: 95 - 97: 24.148 distance: 97 - 98: 31.214 distance: 98 - 99: 10.499 distance: 98 - 101: 23.661 distance: 99 - 100: 4.996 distance: 99 - 102: 12.247 distance: 102 - 103: 9.072 distance: 103 - 104: 21.746 distance: 103 - 106: 11.858 distance: 104 - 105: 10.516 distance: 104 - 113: 9.316 distance: 106 - 107: 7.147 distance: 107 - 108: 7.274 distance: 108 - 109: 10.177 distance: 109 - 110: 14.333 distance: 110 - 111: 14.094 distance: 110 - 112: 5.011 distance: 113 - 114: 8.291 distance: 113 - 119: 20.078 distance: 114 - 115: 6.333 distance: 114 - 117: 38.626 distance: 115 - 116: 10.578 distance: 115 - 120: 13.004 distance: 118 - 119: 11.395 distance: 120 - 121: 11.813 distance: 121 - 122: 27.005 distance: 122 - 123: 31.697 distance: 122 - 124: 12.216 distance: 123 - 137: 25.776