Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 13 14:58:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/07_2023/6ah3_9622_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/07_2023/6ah3_9622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/07_2023/6ah3_9622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/07_2023/6ah3_9622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/07_2023/6ah3_9622_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/07_2023/6ah3_9622_neut.pdb" } resolution = 3.48 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= 0.009 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 449 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 16401 2.51 5 N 5095 2.21 5 O 6659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 760": "NH1" <-> "NH2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I ARG 237": "NH1" <-> "NH2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 83": "NH1" <-> "NH2" Residue "J TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 122": "NH1" <-> "NH2" Residue "K ARG 137": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 28703 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 7861 Classifications: {'RNA': 369} Modifications used: {'rna2p_pur': 28, 'rna2p_pyr': 22, 'rna3p_pur': 160, 'rna3p_pyr': 159} Link IDs: {'rna2p': 50, 'rna3p': 318} Chain: "B" Number of atoms: 6389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6389 Classifications: {'peptide': 784} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 748} Chain breaks: 4 Chain: "C" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1435 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 14, 'TRANS': 160} Chain: "D" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1685 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "E" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1141 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "F" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1272 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "G" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain: "I" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "J" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2260 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain: "K" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1024 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "T" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1712 Classifications: {'RNA': 80} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 39, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 70} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" 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 26565 SG CYS K 90 69.305 82.028 54.180 1.00 53.49 S ATOM 26762 SG CYS K 115 67.908 78.298 50.233 1.00 73.56 S ATOM 26772 SG CYS K 117 66.234 78.409 53.838 1.00 72.07 S Time building chain proxies: 13.73, per 1000 atoms: 0.48 Number of scatterers: 28703 At special positions: 0 Unit cell: (154.44, 130.68, 204.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 96 16.00 P 449 15.00 Mg 2 11.99 O 6659 8.00 N 5095 7.00 C 16401 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: 12.02 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 115 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 90 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 117 " 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 16 sheets defined 43.9% alpha, 16.9% beta 99 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 9.56 Creating SS restraints... Processing helix chain 'B' and resid 58 through 84 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.758A pdb=" N LEU B 92 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.855A pdb=" N SER B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.206A pdb=" N ARG B 107 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 124 removed outlier: 4.291A pdb=" N ASN B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 166 removed outlier: 3.903A pdb=" N SER B 153 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.577A pdb=" N THR B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.767A pdb=" N ILE B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.662A pdb=" N ARG B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 307 through 318 removed outlier: 4.439A pdb=" N LYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 407 through 416 Processing helix chain 'B' and resid 422 through 435 removed outlier: 3.702A pdb=" N GLU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 465 through 469 removed outlier: 4.015A pdb=" N LYS B 468 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 469 " --> pdb=" O GLN B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 465 through 469' Processing helix chain 'B' and resid 471 through 481 removed outlier: 3.913A pdb=" N ILE B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.604A pdb=" N ILE B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.803A pdb=" N ARG B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 564 through 571 removed outlier: 3.572A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 593 Processing helix chain 'B' and resid 597 through 602 removed outlier: 3.739A pdb=" N TYR B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 627 Processing helix chain 'B' and resid 660 through 678 Processing helix chain 'B' and resid 702 through 718 removed outlier: 3.945A pdb=" N VAL B 706 " --> pdb=" O CYS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 798 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 844 through 850 removed outlier: 3.675A pdb=" N GLN B 850 " --> pdb=" O ALA B 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 39 through 42 removed outlier: 3.620A pdb=" N LEU C 42 " --> pdb=" O ASP C 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 39 through 42' Processing helix chain 'C' and resid 43 through 57 removed outlier: 4.688A pdb=" N HIS C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.024A pdb=" N ASN C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.653A pdb=" N LEU C 105 " --> pdb=" O PRO C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.565A pdb=" N CYS C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 150 through 158 removed outlier: 4.917A pdb=" N GLN C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.657A pdb=" N ASN D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 84 through 111 Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.657A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 removed outlier: 3.667A pdb=" N GLU D 131 " --> pdb=" O PRO D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 155 Proline residue: D 141 - end of helix removed outlier: 3.933A pdb=" N GLU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU D 146 " --> pdb=" O MET D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.980A pdb=" N GLY D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 273 removed outlier: 3.912A pdb=" N MET D 273 " --> pdb=" O CYS D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.523A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 62 through 69 Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 123 through 147 Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.871A pdb=" N CYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.645A pdb=" N LYS F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.871A pdb=" N PHE F 98 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.595A pdb=" N ASN F 105 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN F 106 " --> pdb=" O ILE F 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 102 through 106' Processing helix chain 'G' and resid 40 through 59 removed outlier: 4.556A pdb=" N HIS G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 83 removed outlier: 3.888A pdb=" N GLN G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 27 removed outlier: 3.663A pdb=" N ASP H 24 " --> pdb=" O ASP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 45 removed outlier: 3.558A pdb=" N TRP H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 52 Processing helix chain 'H' and resid 73 through 82 removed outlier: 4.116A pdb=" N SER H 80 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 3.764A pdb=" N ASP H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 37 removed outlier: 3.682A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 77 removed outlier: 4.470A pdb=" N LEU I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.711A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 123 removed outlier: 3.663A pdb=" N THR I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.616A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.683A pdb=" N LEU I 164 " --> pdb=" O GLY I 161 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG I 165 " --> pdb=" O TYR I 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 161 through 165' Processing helix chain 'I' and resid 167 through 185 removed outlier: 4.315A pdb=" N ARG I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG I 185 " --> pdb=" O ILE I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 201 removed outlier: 3.503A pdb=" N GLU I 200 " --> pdb=" O SER I 197 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N CYS I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 197 through 201' Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 217 through 242 removed outlier: 4.536A pdb=" N ALA I 229 " --> pdb=" O MET I 225 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU I 234 " --> pdb=" O SER I 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 36 removed outlier: 3.577A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 removed outlier: 4.004A pdb=" N ASP J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 104 removed outlier: 3.542A pdb=" N ILE J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE J 104 " --> pdb=" O ILE J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 removed outlier: 3.863A pdb=" N LEU J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.563A pdb=" N ARG J 165 " --> pdb=" O TYR J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 185 removed outlier: 4.022A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG J 185 " --> pdb=" O ILE J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 removed outlier: 3.766A pdb=" N GLU J 200 " --> pdb=" O SER J 197 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 197 through 201' Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 217 through 227 Processing helix chain 'J' and resid 227 through 241 removed outlier: 3.722A pdb=" N VAL J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY J 236 " --> pdb=" O VAL J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 55 removed outlier: 3.913A pdb=" N ALA K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 77 removed outlier: 3.762A pdb=" N ALA K 63 " --> pdb=" O HIS K 59 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG K 64 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.570A pdb=" N LYS K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.042A pdb=" N GLY B 216 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 393 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 295 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER B 340 " --> pdb=" O PRO B 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 450 removed outlier: 3.672A pdb=" N VAL B 546 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER B 400 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 827 through 830 removed outlier: 4.131A pdb=" N THR B 828 " --> pdb=" O MET B 837 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET B 837 " --> pdb=" O THR B 828 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 841 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 823 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 843 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ILE B 821 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 781 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE B 823 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA B 779 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 18 through 19 removed outlier: 4.030A pdb=" N THR K 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN C 17 " --> pdb=" O THR K 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.915A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 207 through 211 Processing sheet with id=AA9, first strand: chain 'E' and resid 73 through 78 removed outlier: 3.822A pdb=" N GLN E 73 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE E 85 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE E 77 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR E 83 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.287A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.287A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 15 through 17 removed outlier: 6.565A pdb=" N ILE G 33 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N MET G 68 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 55 through 61 removed outlier: 8.772A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR H 11 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU H 102 " --> pdb=" O TYR H 11 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS H 13 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.787A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR I 46 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE I 41 " --> pdb=" O LYS I 79 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU I 110 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU I 86 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL I 107 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N THR I 130 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA I 109 " --> pdb=" O THR I 130 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLY I 192 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE I 158 " --> pdb=" O GLY I 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.278A pdb=" N VAL J 3 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA J 42 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU J 5 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN J 44 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL J 7 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR J 46 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE J 41 " --> pdb=" O TYR J 81 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ARG J 83 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE J 43 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR J 85 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE J 45 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE J 87 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL J 47 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N ILE J 106 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER J 82 " --> pdb=" O ILE J 106 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ALA J 108 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE J 84 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU J 110 " --> pdb=" O ILE J 84 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU J 86 " --> pdb=" O LEU J 110 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL J 107 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR J 130 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA J 109 " --> pdb=" O THR J 130 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 102 through 105 removed outlier: 3.540A pdb=" N LYS K 102 " --> pdb=" O MET K 114 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 253 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 99 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 13.20 Time building geometry restraints manager: 12.64 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: 5546 1.33 - 1.45: 9280 1.45 - 1.58: 14311 1.58 - 1.70: 895 1.70 - 1.82: 146 Bond restraints: 30178 Sorted by residual: bond pdb=" O3' G T 4 " pdb=" P A T 5 " ideal model delta sigma weight residual 1.607 1.504 0.103 1.50e-02 4.44e+03 4.76e+01 bond pdb=" C ILE C 108 " pdb=" N PRO C 109 " ideal model delta sigma weight residual 1.337 1.388 -0.052 1.11e-02 8.12e+03 2.19e+01 bond pdb=" C PHE B 598 " pdb=" N PRO B 599 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" C PRO K 24 " pdb=" N PRO K 25 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 1.01e+01 bond pdb=" N GLN B 331 " pdb=" CA GLN B 331 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.09e+00 ... (remaining 30173 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.36: 2995 106.36 - 113.72: 17761 113.72 - 121.09: 13918 121.09 - 128.45: 7611 128.45 - 135.82: 653 Bond angle restraints: 42938 Sorted by residual: angle pdb=" N ILE I 112 " pdb=" CA ILE I 112 " pdb=" C ILE I 112 " ideal model delta sigma weight residual 113.10 105.89 7.21 9.70e-01 1.06e+00 5.52e+01 angle pdb=" C VAL B 361 " pdb=" N GLN B 362 " pdb=" CA GLN B 362 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" N ASN D 215 " pdb=" CA ASN D 215 " pdb=" C ASN D 215 " ideal model delta sigma weight residual 111.14 105.88 5.26 1.08e+00 8.57e-01 2.38e+01 angle pdb=" N VAL H 111 " pdb=" CA VAL H 111 " pdb=" C VAL H 111 " ideal model delta sigma weight residual 108.82 102.91 5.91 1.22e+00 6.72e-01 2.34e+01 angle pdb=" C3' U A 266 " pdb=" O3' U A 266 " pdb=" P U A 267 " ideal model delta sigma weight residual 120.20 127.41 -7.21 1.50e+00 4.44e-01 2.31e+01 ... (remaining 42933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 16957 35.32 - 70.63: 374 70.63 - 105.95: 29 105.95 - 141.27: 3 141.27 - 176.59: 10 Dihedral angle restraints: 17373 sinusoidal: 10389 harmonic: 6984 Sorted by residual: dihedral pdb=" C4' U A 93 " pdb=" C3' U A 93 " pdb=" C2' U A 93 " pdb=" C1' U A 93 " ideal model delta sinusoidal sigma weight residual -35.00 36.00 -71.00 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" O4' U A 93 " pdb=" C2' U A 93 " pdb=" C1' U A 93 " pdb=" C3' U A 93 " ideal model delta sinusoidal sigma weight residual -35.00 32.84 -67.84 1 8.00e+00 1.56e-02 9.34e+01 dihedral pdb=" O4' U A 329 " pdb=" C1' U A 329 " pdb=" N1 U A 329 " pdb=" C2 U A 329 " ideal model delta sinusoidal sigma weight residual 200.00 42.99 157.01 1 1.50e+01 4.44e-03 8.19e+01 ... (remaining 17370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4696 0.072 - 0.144: 410 0.144 - 0.216: 110 0.216 - 0.288: 4 0.288 - 0.359: 2 Chirality restraints: 5222 Sorted by residual: chirality pdb=" C3' A A 367 " pdb=" C4' A A 367 " pdb=" O3' A A 367 " pdb=" C2' A A 367 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C3' G A 179 " pdb=" C4' G A 179 " pdb=" O3' G A 179 " pdb=" C2' G A 179 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C3' U A 266 " pdb=" C4' U A 266 " pdb=" O3' U A 266 " pdb=" C2' U A 266 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5219 not shown) Planarity restraints: 3770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G T 4 " -0.029 2.00e-02 2.50e+03 2.31e-02 1.60e+01 pdb=" N9 G T 4 " 0.013 2.00e-02 2.50e+03 pdb=" C8 G T 4 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G T 4 " -0.020 2.00e-02 2.50e+03 pdb=" C5 G T 4 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G T 4 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G T 4 " 0.023 2.00e-02 2.50e+03 pdb=" N1 G T 4 " -0.040 2.00e-02 2.50e+03 pdb=" C2 G T 4 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G T 4 " -0.009 2.00e-02 2.50e+03 pdb=" N3 G T 4 " 0.039 2.00e-02 2.50e+03 pdb=" C4 G T 4 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 728 " -0.051 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO B 729 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 729 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 729 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER F 93 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C SER F 93 " -0.047 2.00e-02 2.50e+03 pdb=" O SER F 93 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE F 94 " 0.016 2.00e-02 2.50e+03 ... (remaining 3767 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 16 2.16 - 2.85: 8530 2.85 - 3.53: 36466 3.53 - 4.22: 73409 4.22 - 4.90: 110059 Nonbonded interactions: 228480 Sorted by model distance: nonbonded pdb=" NH2 ARG B 87 " pdb=" O2 C T 2 " model vdw 1.476 2.520 nonbonded pdb=" C5' A A 344 " pdb=" O2' A T 0 " model vdw 1.530 3.440 nonbonded pdb=" O2 U A 311 " pdb=" C5 A A 344 " model vdw 1.725 3.260 nonbonded pdb=" O2' U A 93 " pdb=" O5' C A 94 " model vdw 1.853 2.440 nonbonded pdb=" O2 U A 311 " pdb=" N7 A A 344 " model vdw 1.922 3.120 ... (remaining 228475 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.600 Check model and map are aligned: 0.430 Set scattering table: 0.230 Process input model: 83.460 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5715 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 : 0.004 0.103 30178 Z= 0.226 Angle : 0.829 12.714 42938 Z= 0.485 Chirality : 0.046 0.359 5222 Planarity : 0.006 0.078 3770 Dihedral : 13.189 176.585 12837 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.91 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.57 (0.14), residues: 2350 helix: -2.57 (0.12), residues: 884 sheet: -0.89 (0.24), residues: 430 loop : -2.76 (0.16), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 814 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 816 average time/residue: 0.4842 time to fit residues: 595.3831 Evaluate side-chains 406 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 404 time to evaluate : 2.492 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2596 time to fit residues: 4.4786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 116 optimal weight: 0.0070 chunk 71 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS B 246 ASN B 251 HIS B 323 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN B 590 GLN B 642 HIS B 677 ASN B 701 ASN B 808 HIS ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN F 8 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN F 65 GLN F 87 HIS F 89 GLN F 111 GLN F 113 ASN G 18 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 HIS J 151 ASN J 172 GLN ** J 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 243 HIS K 30 ASN ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 30178 Z= 0.232 Angle : 0.633 12.405 42938 Z= 0.322 Chirality : 0.038 0.263 5222 Planarity : 0.005 0.073 3770 Dihedral : 13.619 177.287 7979 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.40 % Favored : 94.55 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.93 (0.16), residues: 2350 helix: -0.64 (0.16), residues: 919 sheet: -0.56 (0.25), residues: 420 loop : -2.16 (0.18), residues: 1011 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 482 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 47 residues processed: 531 average time/residue: 0.4291 time to fit residues: 354.4561 Evaluate side-chains 397 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 350 time to evaluate : 2.667 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.2729 time to fit residues: 27.4231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 210 optimal weight: 0.1980 chunk 171 optimal weight: 0.0070 chunk 69 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 225 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN D 99 ASN F 37 ASN F 89 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS J 168 GLN K 38 ASN K 42 GLN ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 30178 Z= 0.234 Angle : 0.632 15.541 42938 Z= 0.323 Chirality : 0.038 0.227 5222 Planarity : 0.006 0.080 3770 Dihedral : 13.565 179.663 7979 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.31 (0.17), residues: 2350 helix: 0.13 (0.17), residues: 921 sheet: -0.56 (0.24), residues: 433 loop : -1.95 (0.19), residues: 996 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 462 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 33 residues processed: 503 average time/residue: 0.4160 time to fit residues: 328.0844 Evaluate side-chains 403 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 370 time to evaluate : 2.506 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3047 time to fit residues: 21.9180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 6.9990 chunk 190 optimal weight: 0.3980 chunk 131 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN D 197 GLN E 139 ASN F 89 GLN ** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 ASN J 143 HIS ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 HIS K 140 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.7709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 30178 Z= 0.299 Angle : 0.683 16.507 42938 Z= 0.346 Chirality : 0.040 0.237 5222 Planarity : 0.006 0.073 3770 Dihedral : 13.594 179.526 7979 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 4.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.18 (0.17), residues: 2350 helix: 0.24 (0.16), residues: 937 sheet: -0.65 (0.24), residues: 422 loop : -1.81 (0.19), residues: 991 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 439 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 42 residues processed: 495 average time/residue: 0.4215 time to fit residues: 324.4379 Evaluate side-chains 376 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 334 time to evaluate : 2.540 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2883 time to fit residues: 25.3137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 241 optimal weight: 0.8980 chunk 67 optimal weight: 0.0060 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN B 371 HIS ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 111 GLN H 27 HIS I 34 HIS J 245 GLN K 31 GLN K 42 GLN ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.8118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 30178 Z= 0.191 Angle : 0.575 14.945 42938 Z= 0.294 Chirality : 0.036 0.208 5222 Planarity : 0.005 0.088 3770 Dihedral : 13.381 178.862 7979 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2350 helix: 0.74 (0.17), residues: 940 sheet: -0.47 (0.25), residues: 422 loop : -1.75 (0.20), residues: 988 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 380 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 33 residues processed: 424 average time/residue: 0.4298 time to fit residues: 284.9064 Evaluate side-chains 360 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 327 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2843 time to fit residues: 20.4899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 157 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 22 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN H 70 ASN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 ASN ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.8330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30178 Z= 0.162 Angle : 0.555 14.843 42938 Z= 0.283 Chirality : 0.035 0.206 5222 Planarity : 0.004 0.071 3770 Dihedral : 13.244 179.024 7979 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2350 helix: 0.97 (0.17), residues: 940 sheet: -0.41 (0.25), residues: 429 loop : -1.66 (0.20), residues: 981 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 365 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 26 residues processed: 396 average time/residue: 0.4139 time to fit residues: 259.5021 Evaluate side-chains 354 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 328 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2789 time to fit residues: 16.2492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 HIS ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 99 ASN D 179 ASN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS K 38 ASN ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.8747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30178 Z= 0.191 Angle : 0.568 15.189 42938 Z= 0.290 Chirality : 0.036 0.205 5222 Planarity : 0.004 0.069 3770 Dihedral : 13.233 179.356 7979 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2350 helix: 1.09 (0.17), residues: 938 sheet: -0.46 (0.25), residues: 416 loop : -1.66 (0.20), residues: 996 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 363 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 390 average time/residue: 0.4191 time to fit residues: 257.5328 Evaluate side-chains 349 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 328 time to evaluate : 2.368 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2706 time to fit residues: 13.5634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 9.9990 chunk 107 optimal weight: 0.0010 chunk 160 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 52 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 783 GLN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN C 77 GLN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.8868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 30178 Z= 0.152 Angle : 0.547 14.663 42938 Z= 0.278 Chirality : 0.035 0.207 5222 Planarity : 0.004 0.064 3770 Dihedral : 13.153 178.927 7979 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2350 helix: 1.25 (0.17), residues: 939 sheet: -0.45 (0.25), residues: 424 loop : -1.57 (0.20), residues: 987 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 355 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 364 average time/residue: 0.4091 time to fit residues: 234.9422 Evaluate side-chains 338 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 326 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2503 time to fit residues: 8.8357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 249 optimal weight: 0.0980 chunk 150 optimal weight: 3.9990 chunk 108 optimal weight: 0.0770 chunk 196 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS D 179 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 245 GLN ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.9007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 30178 Z= 0.152 Angle : 0.546 14.523 42938 Z= 0.276 Chirality : 0.035 0.195 5222 Planarity : 0.004 0.061 3770 Dihedral : 13.078 178.777 7979 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2350 helix: 1.36 (0.17), residues: 937 sheet: -0.35 (0.25), residues: 431 loop : -1.55 (0.20), residues: 982 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 345 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 353 average time/residue: 0.4317 time to fit residues: 240.5172 Evaluate side-chains 328 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 322 time to evaluate : 2.760 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2613 time to fit residues: 6.7941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 0.6980 chunk 264 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 276 optimal weight: 10.0000 chunk 254 optimal weight: 20.0000 chunk 220 optimal weight: 0.9980 chunk 22 optimal weight: 30.0000 chunk 170 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 783 GLN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.9428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 30178 Z= 0.197 Angle : 0.585 15.419 42938 Z= 0.296 Chirality : 0.036 0.204 5222 Planarity : 0.004 0.062 3770 Dihedral : 13.113 179.057 7979 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2350 helix: 1.23 (0.17), residues: 941 sheet: -0.39 (0.26), residues: 419 loop : -1.51 (0.20), residues: 990 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 344 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 350 average time/residue: 0.4228 time to fit residues: 233.9921 Evaluate side-chains 332 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 323 time to evaluate : 2.674 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4138 time to fit residues: 9.5475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 226 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 179 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.169956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.131814 restraints weight = 46373.717| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.11 r_work: 0.3481 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.9562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 30178 Z= 0.173 Angle : 0.562 14.860 42938 Z= 0.285 Chirality : 0.036 0.237 5222 Planarity : 0.005 0.099 3770 Dihedral : 13.044 178.618 7979 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2350 helix: 1.32 (0.17), residues: 943 sheet: -0.35 (0.26), residues: 419 loop : -1.55 (0.20), residues: 988 =============================================================================== Job complete usr+sys time: 6230.94 seconds wall clock time: 114 minutes 32.39 seconds (6872.39 seconds total)