Starting phenix.real_space_refine on Tue Feb 20 18:06:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/02_2024/6ah3_9622_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/02_2024/6ah3_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_9622/02_2024/6ah3_9622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/02_2024/6ah3_9622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/02_2024/6ah3_9622_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ah3_9622/02_2024/6ah3_9622_neut.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 15.74, per 1000 atoms: 0.55 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: 12.28 Conformation dependent library (CDL) restraints added in 3.3 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: 9.59 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: 12.37 Time building geometry restraints manager: 13.13 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: 17706 35.32 - 70.63: 1166 70.63 - 105.95: 130 105.95 - 141.27: 3 141.27 - 176.59: 10 Dihedral angle restraints: 19015 sinusoidal: 12031 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 19012 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: 0.730 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: 5.480 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 85.110 Find NCS groups from input model: 0.700 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: 0.010 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.080 ------------------------------------------------------------------------------- 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 : 19.187 176.585 14479 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 % Allowed : 3.00 % Favored : 96.81 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 44 HIS 0.007 0.001 HIS B 273 PHE 0.031 0.002 PHE D 207 TYR 0.025 0.002 TYR B 597 ARG 0.011 0.001 ARG B 97 *********************** 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 : 2.770 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 REVERT: B 168 LEU cc_start: 0.6786 (pp) cc_final: 0.6550 (pp) REVERT: B 397 SER cc_start: 0.7668 (p) cc_final: 0.7433 (p) REVERT: C 95 ASN cc_start: 0.4908 (OUTLIER) cc_final: 0.4205 (t0) REVERT: D 277 ILE cc_start: 0.4970 (mm) cc_final: 0.4178 (mt) REVERT: I 158 ILE cc_start: 0.8527 (mt) cc_final: 0.7832 (mt) REVERT: I 204 ILE cc_start: 0.7760 (tt) cc_final: 0.7530 (tt) REVERT: J 261 ASN cc_start: 0.7521 (m-40) cc_final: 0.7250 (m-40) outliers start: 4 outliers final: 2 residues processed: 816 average time/residue: 0.4685 time to fit residues: 573.1962 Evaluate side-chains 408 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 405 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain C residue 95 ASN 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: 0.6980 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: 0.8980 chunk 132 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 ASN B 701 ASN B 808 HIS C 25 ASN ** C 95 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30178 Z= 0.236 Angle : 0.641 10.605 42938 Z= 0.325 Chirality : 0.038 0.273 5222 Planarity : 0.005 0.068 3770 Dihedral : 21.549 178.418 9626 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 4.20 % Allowed : 13.63 % Favored : 82.17 % 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: -1.88 (0.16), residues: 2350 helix: -0.59 (0.16), residues: 917 sheet: -0.61 (0.24), residues: 433 loop : -2.12 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 44 HIS 0.008 0.001 HIS J 34 PHE 0.025 0.002 PHE I 104 TYR 0.021 0.002 TYR K 134 ARG 0.010 0.001 ARG G 47 *********************** 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 583 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 492 time to evaluate : 2.546 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: B 79 ASN cc_start: 0.7840 (t0) cc_final: 0.7628 (t0) REVERT: B 452 ASP cc_start: 0.7054 (t0) cc_final: 0.6821 (t0) REVERT: B 720 MET cc_start: 0.3092 (mpp) cc_final: 0.1470 (ptt) REVERT: C 125 PRO cc_start: 0.5683 (Cg_endo) cc_final: 0.5355 (Cg_exo) REVERT: E 125 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8077 (mmtm) REVERT: E 135 SER cc_start: 0.8411 (t) cc_final: 0.7767 (m) REVERT: E 136 LYS cc_start: 0.8585 (mttt) cc_final: 0.8376 (mtmm) REVERT: E 142 LYS cc_start: 0.7487 (mmtp) cc_final: 0.7175 (mmmt) REVERT: F 94 ILE cc_start: 0.6333 (mp) cc_final: 0.6008 (mp) REVERT: F 110 TYR cc_start: 0.6556 (m-80) cc_final: 0.6341 (m-80) REVERT: H 31 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6837 (tm-30) REVERT: H 51 GLU cc_start: 0.6860 (tt0) cc_final: 0.6519 (tt0) REVERT: H 111 VAL cc_start: 0.4419 (OUTLIER) cc_final: 0.4115 (t) REVERT: I 110 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7183 (tp) REVERT: I 146 ILE cc_start: 0.6807 (mm) cc_final: 0.6569 (mm) outliers start: 91 outliers final: 49 residues processed: 546 average time/residue: 0.4158 time to fit residues: 353.0956 Evaluate side-chains 411 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 360 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 869 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 62 LEU 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: 0.0970 chunk 210 optimal weight: 10.0000 chunk 171 optimal weight: 0.0060 chunk 69 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 225 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 202 optimal weight: 0.0570 overall best weight: 1.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 665 GLN C 123 GLN D 99 ASN F 37 ASN G 58 GLN ** 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** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30178 Z= 0.207 Angle : 0.598 15.205 42938 Z= 0.305 Chirality : 0.037 0.214 5222 Planarity : 0.005 0.061 3770 Dihedral : 21.267 177.354 9622 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.06 % Allowed : 17.09 % Favored : 78.85 % 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: -1.17 (0.17), residues: 2350 helix: 0.24 (0.17), residues: 927 sheet: -0.56 (0.24), residues: 447 loop : -1.86 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 44 HIS 0.007 0.001 HIS B 273 PHE 0.021 0.002 PHE B 657 TYR 0.018 0.002 TYR J 81 ARG 0.011 0.001 ARG C 148 *********************** 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 530 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 442 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.7858 (t0) cc_final: 0.7649 (t0) REVERT: B 204 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7428 (tp) REVERT: B 452 ASP cc_start: 0.7604 (t0) cc_final: 0.7253 (t0) REVERT: B 758 PHE cc_start: 0.6324 (m-80) cc_final: 0.6030 (m-80) REVERT: B 803 ASN cc_start: 0.8345 (t0) cc_final: 0.7924 (t0) REVERT: C 125 PRO cc_start: 0.5838 (Cg_endo) cc_final: 0.5564 (Cg_exo) REVERT: C 133 LYS cc_start: 0.5166 (mttt) cc_final: 0.4831 (mttp) REVERT: C 140 MET cc_start: 0.3807 (mmp) cc_final: 0.3566 (mmp) REVERT: D 106 LEU cc_start: 0.8112 (mt) cc_final: 0.6993 (tp) REVERT: D 151 ILE cc_start: 0.7717 (mm) cc_final: 0.7411 (mm) REVERT: D 233 GLU cc_start: 0.7426 (tt0) cc_final: 0.7163 (tt0) REVERT: E 50 GLN cc_start: 0.7031 (pp30) cc_final: 0.6791 (pt0) REVERT: E 142 LYS cc_start: 0.7613 (mmtp) cc_final: 0.7392 (mtpt) REVERT: F 94 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7176 (mp) REVERT: G 33 ILE cc_start: 0.9070 (mt) cc_final: 0.8832 (mt) REVERT: H 31 GLN cc_start: 0.7449 (tm-30) cc_final: 0.7068 (tm-30) REVERT: H 37 TRP cc_start: 0.8631 (t60) cc_final: 0.8333 (t60) REVERT: I 110 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8449 (tp) outliers start: 88 outliers final: 54 residues processed: 501 average time/residue: 0.4231 time to fit residues: 330.0659 Evaluate side-chains 405 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 348 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 65 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 595 GLN C 40 GLN C 158 GLN D 179 ASN E 139 ASN ** 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** J 44 ASN ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.8235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 30178 Z= 0.376 Angle : 0.776 17.969 42938 Z= 0.395 Chirality : 0.043 0.243 5222 Planarity : 0.006 0.077 3770 Dihedral : 21.341 178.984 9622 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.89 % Favored : 93.06 % Rotamer: Outliers : 6.14 % Allowed : 17.00 % Favored : 76.86 % 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: -1.40 (0.17), residues: 2350 helix: 0.09 (0.17), residues: 926 sheet: -0.76 (0.25), residues: 412 loop : -1.94 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 66 HIS 0.009 0.002 HIS E 36 PHE 0.041 0.003 PHE B 657 TYR 0.033 0.003 TYR K 66 ARG 0.011 0.001 ARG B 321 *********************** 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 570 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 437 time to evaluate : 2.545 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: B 152 MET cc_start: 0.8237 (mmm) cc_final: 0.7928 (mmp) REVERT: B 333 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8982 (tt) REVERT: B 720 MET cc_start: 0.3794 (mpp) cc_final: 0.1470 (ptt) REVERT: B 768 THR cc_start: 0.8760 (p) cc_final: 0.8542 (p) REVERT: B 786 GLU cc_start: 0.8302 (pm20) cc_final: 0.7988 (pt0) REVERT: B 793 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8705 (mp) REVERT: B 821 ILE cc_start: 0.8607 (pt) cc_final: 0.8297 (pt) REVERT: B 835 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.7912 (p0) REVERT: C 125 PRO cc_start: 0.5829 (Cg_endo) cc_final: 0.5055 (Cg_exo) REVERT: C 129 MET cc_start: 0.4267 (mtp) cc_final: 0.3452 (tpp) REVERT: D 91 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6541 (mt-10) REVERT: D 167 SER cc_start: 0.8661 (t) cc_final: 0.8175 (m) REVERT: D 204 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8909 (t) REVERT: D 238 ASP cc_start: 0.4286 (OUTLIER) cc_final: 0.2718 (p0) REVERT: E 8 TYR cc_start: 0.7945 (m-80) cc_final: 0.7458 (m-10) REVERT: E 101 MET cc_start: 0.8169 (tmm) cc_final: 0.7940 (tmm) REVERT: E 134 ASN cc_start: 0.8460 (m-40) cc_final: 0.8246 (m110) REVERT: F 94 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8830 (mp) REVERT: G 58 GLN cc_start: 0.8403 (tp-100) cc_final: 0.7965 (tp40) REVERT: H 31 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7412 (tm-30) REVERT: H 44 ARG cc_start: 0.7520 (tpp-160) cc_final: 0.7215 (tpp-160) REVERT: H 119 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8134 (mm) REVERT: I 5 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8079 (pp) REVERT: I 81 TYR cc_start: 0.8064 (m-80) cc_final: 0.7860 (m-80) REVERT: J 76 THR cc_start: 0.8194 (m) cc_final: 0.7885 (m) REVERT: J 122 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8506 (p) REVERT: J 157 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: J 186 SER cc_start: 0.8956 (m) cc_final: 0.8671 (t) outliers start: 133 outliers final: 67 residues processed: 526 average time/residue: 0.4181 time to fit residues: 342.3337 Evaluate side-chains 420 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 342 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 835 ASN Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 157 GLU Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain K residue 32 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN B 665 GLN ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 126 HIS D 179 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** H 27 HIS ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 203 ASN I 240 ASN J 34 HIS J 245 GLN K 38 ASN ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.8551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30178 Z= 0.201 Angle : 0.589 16.426 42938 Z= 0.300 Chirality : 0.037 0.213 5222 Planarity : 0.005 0.087 3770 Dihedral : 21.229 178.303 9622 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.90 % Allowed : 20.83 % Favored : 74.27 % 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: -0.86 (0.18), residues: 2350 helix: 0.65 (0.17), residues: 939 sheet: -0.55 (0.25), residues: 416 loop : -1.77 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 66 HIS 0.007 0.001 HIS B 844 PHE 0.024 0.002 PHE B 657 TYR 0.022 0.002 TYR F 110 ARG 0.008 0.001 ARG B 66 *********************** 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 495 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 389 time to evaluate : 2.618 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: B 645 LYS cc_start: 0.7996 (pptt) cc_final: 0.7676 (mmtt) REVERT: B 665 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: B 793 LEU cc_start: 0.8947 (mt) cc_final: 0.8693 (mp) REVERT: C 113 TYR cc_start: 0.5896 (t80) cc_final: 0.5684 (t80) REVERT: D 91 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6373 (mt-10) REVERT: D 167 SER cc_start: 0.8511 (t) cc_final: 0.8069 (m) REVERT: D 238 ASP cc_start: 0.4123 (OUTLIER) cc_final: 0.2713 (p0) REVERT: E 12 GLU cc_start: 0.7215 (tt0) cc_final: 0.6909 (tt0) REVERT: E 101 MET cc_start: 0.8246 (tmm) cc_final: 0.8008 (tmm) REVERT: E 124 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8362 (ttpt) REVERT: F 94 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8668 (mp) REVERT: G 58 GLN cc_start: 0.8237 (tp-100) cc_final: 0.8021 (tp40) REVERT: G 118 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6889 (tm-30) REVERT: H 31 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7535 (tm-30) REVERT: I 5 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7841 (pp) REVERT: I 81 TYR cc_start: 0.8170 (m-80) cc_final: 0.7853 (m-80) REVERT: I 225 MET cc_start: 0.5493 (tmm) cc_final: 0.5175 (tpp) REVERT: J 75 ARG cc_start: 0.6704 (ttp80) cc_final: 0.6441 (ptt90) REVERT: J 137 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8337 (mt) REVERT: J 157 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7370 (tt0) REVERT: J 225 MET cc_start: 0.5059 (mmp) cc_final: 0.4573 (ttm) outliers start: 106 outliers final: 62 residues processed: 466 average time/residue: 0.4172 time to fit residues: 307.8936 Evaluate side-chains 422 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 353 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 268 optimal weight: 0.2980 chunk 223 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 22 optimal weight: 30.0000 chunk 88 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 139 ASN F 106 ASN ** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.8805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30178 Z= 0.189 Angle : 0.577 16.590 42938 Z= 0.294 Chirality : 0.036 0.201 5222 Planarity : 0.005 0.094 3770 Dihedral : 21.144 178.371 9622 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.62 % Allowed : 22.08 % Favored : 73.30 % 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: -0.68 (0.18), residues: 2350 helix: 0.85 (0.17), residues: 943 sheet: -0.57 (0.25), residues: 418 loop : -1.67 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 66 HIS 0.005 0.001 HIS B 844 PHE 0.024 0.002 PHE D 253 TYR 0.017 0.002 TYR F 110 ARG 0.007 0.001 ARG B 325 *********************** 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 457 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 357 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 LYS cc_start: 0.7965 (pptt) cc_final: 0.7695 (mmtt) REVERT: B 793 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8745 (mp) REVERT: B 858 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7546 (ttp80) REVERT: C 33 MET cc_start: 0.4391 (mmt) cc_final: 0.4175 (mmt) REVERT: D 91 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6382 (mt-10) REVERT: D 167 SER cc_start: 0.8523 (t) cc_final: 0.8078 (m) REVERT: D 208 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6206 (t80) REVERT: D 253 PHE cc_start: 0.7211 (p90) cc_final: 0.6851 (p90) REVERT: E 12 GLU cc_start: 0.7238 (tt0) cc_final: 0.6773 (tt0) REVERT: E 101 MET cc_start: 0.8204 (tmm) cc_final: 0.7940 (tmm) REVERT: E 124 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8357 (ttpt) REVERT: F 94 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8799 (mp) REVERT: F 106 ASN cc_start: 0.6529 (OUTLIER) cc_final: 0.6320 (p0) REVERT: G 58 GLN cc_start: 0.8250 (tp-100) cc_final: 0.8025 (tp40) REVERT: H 31 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7589 (tm-30) REVERT: H 117 LEU cc_start: 0.7372 (tt) cc_final: 0.7076 (tp) REVERT: I 81 TYR cc_start: 0.8124 (m-80) cc_final: 0.7861 (m-80) REVERT: J 225 MET cc_start: 0.5330 (mmp) cc_final: 0.4835 (ttm) REVERT: K 70 MET cc_start: 0.8138 (ttp) cc_final: 0.7920 (ttt) outliers start: 100 outliers final: 75 residues processed: 424 average time/residue: 0.3954 time to fit residues: 269.2642 Evaluate side-chains 409 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 327 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 858 ARG Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 60 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 226 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 ASN ** 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 466 GLN B 803 ASN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN F 113 ASN ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS J 34 HIS ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.9030 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= 0.175 Angle : 0.559 15.648 42938 Z= 0.285 Chirality : 0.036 0.198 5222 Planarity : 0.004 0.094 3770 Dihedral : 21.086 178.242 9622 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.99 % Allowed : 22.40 % Favored : 72.61 % 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: 1.05 (0.17), residues: 946 sheet: -0.44 (0.25), residues: 421 loop : -1.65 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 66 HIS 0.005 0.001 HIS B 273 PHE 0.017 0.002 PHE B 657 TYR 0.024 0.001 TYR F 110 ARG 0.008 0.001 ARG I 136 *********************** 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 461 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 353 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 LYS cc_start: 0.7923 (pptt) cc_final: 0.7502 (mmtt) REVERT: B 793 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8761 (mp) REVERT: C 68 LEU cc_start: 0.4545 (OUTLIER) cc_final: 0.4059 (pp) REVERT: D 91 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6390 (mt-10) REVERT: D 167 SER cc_start: 0.8531 (t) cc_final: 0.8099 (m) REVERT: D 208 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6154 (t80) REVERT: E 62 ASP cc_start: 0.5917 (m-30) cc_final: 0.5643 (m-30) REVERT: E 101 MET cc_start: 0.8243 (tmm) cc_final: 0.7970 (tmm) REVERT: E 124 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8364 (ttpt) REVERT: G 58 GLN cc_start: 0.8250 (tp-100) cc_final: 0.8024 (tp40) REVERT: H 99 ILE cc_start: 0.8979 (mt) cc_final: 0.8768 (mt) REVERT: I 45 PHE cc_start: 0.8611 (t80) cc_final: 0.8364 (t80) REVERT: I 81 TYR cc_start: 0.8197 (m-80) cc_final: 0.7914 (m-80) REVERT: J 137 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8364 (mt) REVERT: J 157 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7449 (tt0) REVERT: J 225 MET cc_start: 0.5367 (mmp) cc_final: 0.4848 (ttm) outliers start: 108 outliers final: 84 residues processed: 429 average time/residue: 0.3791 time to fit residues: 263.4210 Evaluate side-chains 420 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 330 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain J residue 286 HIS Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 170 optimal weight: 0.0030 chunk 182 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 ASN ** 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 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 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** D 179 ASN E 139 ASN ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 HIS K 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.9233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30178 Z= 0.178 Angle : 0.562 16.089 42938 Z= 0.286 Chirality : 0.036 0.196 5222 Planarity : 0.004 0.099 3770 Dihedral : 21.046 178.172 9622 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.71 % Allowed : 22.77 % Favored : 72.52 % 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: -0.39 (0.18), residues: 2350 helix: 1.15 (0.17), residues: 944 sheet: -0.41 (0.25), residues: 419 loop : -1.60 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 66 HIS 0.008 0.001 HIS B 273 PHE 0.018 0.002 PHE B 657 TYR 0.020 0.001 TYR F 110 ARG 0.008 0.001 ARG J 277 *********************** 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 456 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 354 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 LYS cc_start: 0.7987 (pptt) cc_final: 0.7537 (mmtt) REVERT: B 786 GLU cc_start: 0.8489 (pm20) cc_final: 0.8016 (pt0) REVERT: B 793 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8807 (mp) REVERT: B 858 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7559 (ttp80) REVERT: C 68 LEU cc_start: 0.4652 (OUTLIER) cc_final: 0.4149 (pp) REVERT: D 91 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6400 (mt-10) REVERT: D 167 SER cc_start: 0.8548 (t) cc_final: 0.8115 (m) REVERT: D 208 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6141 (t80) REVERT: D 238 ASP cc_start: 0.4813 (OUTLIER) cc_final: 0.3570 (p0) REVERT: E 12 GLU cc_start: 0.6970 (tt0) cc_final: 0.6612 (tt0) REVERT: E 101 MET cc_start: 0.8249 (tmm) cc_final: 0.7981 (tmm) REVERT: E 124 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8372 (ttpt) REVERT: F 30 VAL cc_start: 0.8976 (t) cc_final: 0.8741 (p) REVERT: H 107 ARG cc_start: 0.5251 (mmt90) cc_final: 0.5026 (mpt180) REVERT: I 45 PHE cc_start: 0.8599 (t80) cc_final: 0.8368 (t80) REVERT: I 81 TYR cc_start: 0.8224 (m-80) cc_final: 0.7944 (m-80) REVERT: I 157 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7984 (tm-30) REVERT: I 238 LEU cc_start: 0.8168 (tt) cc_final: 0.7815 (mt) REVERT: J 137 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8390 (mt) REVERT: J 225 MET cc_start: 0.5166 (mmp) cc_final: 0.4927 (ttm) REVERT: K 70 MET cc_start: 0.8188 (ttp) cc_final: 0.7939 (ttt) outliers start: 102 outliers final: 77 residues processed: 422 average time/residue: 0.3746 time to fit residues: 255.1034 Evaluate side-chains 419 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 334 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 858 ARG Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 196 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 ASN ** 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 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN C 158 GLN D 179 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN E 139 ASN F 106 ASN H 10 GLN J 34 HIS K 33 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.9429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30178 Z= 0.162 Angle : 0.548 15.395 42938 Z= 0.278 Chirality : 0.035 0.193 5222 Planarity : 0.004 0.103 3770 Dihedral : 20.989 177.761 9622 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.39 % Allowed : 23.46 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2350 helix: 1.25 (0.17), residues: 950 sheet: -0.36 (0.25), residues: 435 loop : -1.54 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 66 HIS 0.007 0.001 HIS B 273 PHE 0.018 0.002 PHE B 657 TYR 0.017 0.001 TYR F 110 ARG 0.006 0.000 ARG J 277 *********************** 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 445 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 350 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 LYS cc_start: 0.7801 (pptt) cc_final: 0.7418 (mmtt) REVERT: B 793 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8830 (mp) REVERT: C 68 LEU cc_start: 0.4642 (OUTLIER) cc_final: 0.4149 (pp) REVERT: D 91 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6408 (mt-10) REVERT: D 167 SER cc_start: 0.8532 (t) cc_final: 0.8100 (m) REVERT: D 208 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6256 (t80) REVERT: D 238 ASP cc_start: 0.5377 (OUTLIER) cc_final: 0.4985 (p0) REVERT: E 12 GLU cc_start: 0.7022 (tt0) cc_final: 0.6674 (tt0) REVERT: E 59 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7846 (t0) REVERT: E 101 MET cc_start: 0.8192 (tmm) cc_final: 0.7991 (tmm) REVERT: E 124 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8556 (ttpt) REVERT: F 30 VAL cc_start: 0.8964 (t) cc_final: 0.8761 (p) REVERT: F 106 ASN cc_start: 0.5995 (OUTLIER) cc_final: 0.5746 (p0) REVERT: F 110 TYR cc_start: 0.7871 (m-80) cc_final: 0.7660 (m-10) REVERT: H 107 ARG cc_start: 0.5124 (mmt90) cc_final: 0.4895 (mpt180) REVERT: I 81 TYR cc_start: 0.8214 (m-80) cc_final: 0.7931 (m-80) REVERT: I 238 LEU cc_start: 0.8161 (tt) cc_final: 0.7786 (mt) REVERT: J 157 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: J 225 MET cc_start: 0.5395 (mmp) cc_final: 0.4992 (ttm) REVERT: K 70 MET cc_start: 0.8137 (ttp) cc_final: 0.7895 (ttt) REVERT: K 78 LYS cc_start: 0.7343 (mtmm) cc_final: 0.7036 (mtmm) outliers start: 95 outliers final: 72 residues processed: 412 average time/residue: 0.3743 time to fit residues: 251.5626 Evaluate side-chains 413 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 332 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 27 HIS Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 157 GLU Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 286 HIS Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 2.9990 chunk 264 optimal weight: 0.0770 chunk 161 optimal weight: 0.4980 chunk 125 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 170 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 ASN ** 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 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN F 106 ASN J 34 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.9573 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= 0.177 Angle : 0.561 15.983 42938 Z= 0.284 Chirality : 0.036 0.281 5222 Planarity : 0.004 0.105 3770 Dihedral : 20.961 177.746 9622 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.70 % Allowed : 23.97 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2350 helix: 1.25 (0.17), residues: 955 sheet: -0.36 (0.26), residues: 427 loop : -1.54 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 66 HIS 0.006 0.001 HIS B 273 PHE 0.019 0.002 PHE B 657 TYR 0.027 0.001 TYR D 130 ARG 0.012 0.001 ARG J 277 ********************** 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 422 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 342 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 LYS cc_start: 0.7834 (pptt) cc_final: 0.7466 (mmtt) REVERT: B 793 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8855 (mp) REVERT: C 68 LEU cc_start: 0.4657 (OUTLIER) cc_final: 0.4167 (pp) REVERT: D 91 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6420 (mt-10) REVERT: D 167 SER cc_start: 0.8539 (t) cc_final: 0.8121 (m) REVERT: D 208 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6203 (t80) REVERT: E 12 GLU cc_start: 0.7051 (tt0) cc_final: 0.6691 (tt0) REVERT: E 59 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.7875 (t0) REVERT: E 101 MET cc_start: 0.8206 (tmm) cc_final: 0.7909 (tmm) REVERT: E 124 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8571 (ttpt) REVERT: I 81 TYR cc_start: 0.8213 (m-80) cc_final: 0.7931 (m-80) REVERT: I 238 LEU cc_start: 0.8136 (tt) cc_final: 0.7773 (mt) REVERT: J 157 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: K 70 MET cc_start: 0.8139 (ttp) cc_final: 0.7868 (ttt) outliers start: 80 outliers final: 72 residues processed: 394 average time/residue: 0.3807 time to fit residues: 244.9931 Evaluate side-chains 413 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 334 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 27 HIS Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 157 GLU Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 286 HIS Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 226 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN D 179 ASN E 59 ASN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.165465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126996 restraints weight = 46381.980| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.05 r_work: 0.3413 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.9893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30178 Z= 0.226 Angle : 0.596 16.416 42938 Z= 0.303 Chirality : 0.037 0.195 5222 Planarity : 0.005 0.110 3770 Dihedral : 20.971 177.784 9622 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.93 % Allowed : 23.70 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2350 helix: 1.19 (0.17), residues: 948 sheet: -0.40 (0.25), residues: 430 loop : -1.53 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 66 HIS 0.007 0.001 HIS B 273 PHE 0.024 0.002 PHE H 49 TYR 0.016 0.002 TYR F 110 ARG 0.009 0.001 ARG E 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6543.75 seconds wall clock time: 119 minutes 35.43 seconds (7175.43 seconds total)